After seizing power and then needing to defend it, the Bolsheviks faced a dilemma. They had always openly espoused a citizen-led army, and often extolled the virtues of irregular operations compared to traditional armed forces. But once fighting started in earnest in the civil war it became clear that partisans were both ineffective militarily and were a major challenge to them politically.
The result was a two-faced strategy. Partisans behind enemy lines were supported politically, and occasionally materially, if they were not opposed to Soviet power. Once the Red Army reached them, however, any partisan unit was quickly absorbed into the regular army – and its leaders sent elsewhere to break the personal connections.
Bolshevik propaganda after the war tended to gloss over this process. To show that the Communists had won the war due to their popularity with the people it tended to describe any partisan operations behind White lines as being Red, when most were as firmly anti-Bolshevik as they were anti-White – the so-called "Greens" (or if anarchist, "Blacks"). But in the Soviet nomenclature of the time only pro-Soviets get called partisans, and those that refused to join the Red Army once it reached them were instead "bandits" or "gangsters".
To show how much partisan activity was taking place behind Soviet lines, we can look at the order of Western Front Commander Egorov for 23 March 1920
... 7) In view of the acute situation of the internal front, given that it will intensify even more with the beginning of summer, when gangs of bandits will have the opportunity to widely develop their actions, hiding in the forests, strengthening the rear of the front is a matter of great national importance no less than the position of the external front. At least four divisions are required for this. ...
In the Ukraine the Red-leaning partisans were absorbed in the initial drive across the Ukraine by the Red Army. When the Soviets fell back those that remained were largely nationalist (mostly UNR) or were attached to Makhno, Zelenyi or the like, because known Communist activists had a short lifespan in White held territory. Denikin did not face large organised Soviet resistance in his rear – although there was more than enough Greens and Blacks, of course.
Between the Ukraine and the Urals any Red partisans were also quickly absorbed into regular units early in the war. In particular the Soviets were desperate for cavalry, so any "Red" Cossacks were used as the basis for that arm.
Some of these units continued to have "partisan" in their names long after they were regular army, which does confuse matters.
The brutality of the Whites, and especially the Cossacks, drove many Siberian peasants into opposition from fairly early in the civil war. That they fought the Whites, did not mean that most of them were Red, and indeed many of the same men later also opposed Soviet power. The Bolsheviks did have some success recruiting, but later Soviet literature greatly enlarged the significance of the partisans such as Kravchenko and Shchetinkin, as if they were serious military threats in the manner of Makhno. In reality no Siberian group came close to being able to defeat large regular formations in the way he could.
All the partisan groups anywhere (Red, White, Green or Black) struggled to get men to operate away from their homes. In the Ukraine or Antonov's Tambov, that still allowed sizable forces to be gathered from nearby villages. In the vast distances and rugged terrain of eastern Siberia that was not the case. Kravchenko may well have had 8,000 men by late 1919, but the area around Krasnoyarsk that he operated in was bigger than Texas. That did not allow more than a tiny fraction of them to be working together at any one time.
On top of this, the Siberian partisans were tragically short of weapons – many didn't even have a firearm – and ammunition, had little military training and no firm command structure. (Officially they often formed "regiments" and even higher structures, but the commanders had no experience of leading such units, and the issues of localism and partizanshchina always reappeared.) They were therefore incapable of much by way of collective operations and could not stand in the field against any significant opponent. However their mobility and ability to retreat into the taiga made them very hard to eradicate.
A war of stalemate ensued. The Whites would send out punitive missions, sometimes catching up with and defeating the partisans, but normally the enemy melted away, only to reappear later. Partisan success was obtained by ambushes and beseiging isolated garrisons, not by taking on regular formations. Neither side was able to definitively defeat the other, despite occasional victories.
However, while enormous areas of eastern Siberia were under partisan control, this was of little consequence to Kolchak. His control east of Tomsk was limited anyway, as the real White powers in the area were the Cossack warlords such as Semenov and Kalmykov. The partisans did tie down a large number of men on the vital Trans-Siberian rail-line, but since it was guarded largely by foreign units (Czecho-Slovaks, Poles, Japanese and Americans) who refused to serve in Kolchak's front lines anyway, he did not lose much useful manpower.
By late 1919 it was clear that the Kolchak regime was failing. At that point the partisans started to capture towns and defeat White regulars. Men flocked to be on the winning side.
Kolchak beaten, the puppet "Far Eastern Republic" was established in April 1920 to allow the Soviets to deal at arms' length with the Japanese and remaining Whites. However, its armed forces were merely disguised the Red Army. In order to allow itself to break some of their agreements, those men were sometimes required to pretend to be partisans.
In the very early war any available unit regardless of quality was thrown at the front, but after that it was rare to see partisans fighting alongside regular Red units. Sometimes "partisans" were listed in regular formations. I believe these are irregular units sent behind enemy lines, so operating independently, or simply former partisans whose unit had not yet been renamed.
Partisans were almost always very poorly armed, sometimes not having rifles at all. Some were cavalry.
The one major exception was during Nikifor Grigoriev's campaigns in the Ukraine in early 1919, when he managed to take control of some regular Red Army alongside his units originally formed as partisans. Because he was able to arm and supply them, they became capable of operating outside their local area. Of course, they weren't actually fighting for the Soviets.
Pavel Dybenko may have done the same in the Crimea, when he set up his bizarre "Crimean Soviet Army".
Makhno did ally himself a couple of times with the Soviets, but he always kept his forces completely separate, and it would be anachronistic to mix his units with Red Army ones.
Siberian Partisans in the Civil War by David Footman, St Anthony's Papers Number 1, Soviet Affairs Number One, 1956.
One of the few non-Soviet discussions about partisans. He is quite dismissive of their prowess.
La Guerre en Russie et en Siberie by Ludovic Grondijs.
Grondijs spent some time with the Japanese and discusses the methods of the eastern Siberian partisans in some detail.
The Partisan movement in Siberia during the Civil War, Larkov N.S., Shishkin V.I., Power and society in Siberia in the XX century, Issue 4, Novosibirsk: Parallel, 2013, pp. 76–114This extremely thorough article proposes that the Siberian Partisans were a major force, and severely impeded Kolchak. Unlike most Soviet era works it does balance out their weaknesses and defeats, as well as their strengths and victories.