When Russia started conquering and settling to the east of the Ural mountains and out of Europe into Asia all the way to the Pacific ocean, was it a state project accomplished by the tzar's army, or a private company project accomplished with contractors? Were the settlers peasants relocated there, or volunteers working for work/land? Was the area largely empty of permanent cities, or was it full of khanates and sultanates that were defeated and conquered?
There is no short answer to this as the situation differed depending on both period and geography.
The initial conquest of Siberia made possible by the fall of Kazan in 1552, would resemble very much the Spanish Conquest of the Americas, that took place just about the same time, so one could find good parallels.
In the early stages, the venture would usually be organized and financed by some magnate and led by some seasoned war dog - the classical example is Yermak Timofeyevich and the Stroganovs. The lands were claimed in the name of the Tzar, yet the expeditions were mostly private ventures. The party would usually be quite a colorful mix of cossacks, former soldiers, mercenaries and even prisoners of war - for example, there were Lithuanian and Baltic German soldiers captured during the Livonian war in Yermaks expedition.
This kind of exploration / conquest would continue right up to the beginning of XVIII century. The Russian settlements were sparse and resembled more of the fortified outposts used mostly for fur trade with the locals.
Come Peter I, several major things would happen - Siberia would fall under official administrative division of the state, thus governmental, tax and customs institutions would start finding their way there. Then came the industry - Demidov iron works most notably. And the church reform gave birth to the Old Bellievers (Starovery) who ran from the persecution and would make a significant part of the Russian population in Siberia up until XIXc.
Aboriginal tribes and Khanates were almost fully subdued by the end of the XVIIIc.
Nevertheless, because of the serfdom, the population mobility in Russia at that time was very low and Siberia remained very sparsely populated up until XIXc.
The next big change came with the beginning of construction of the Trans Siberian Railway in 1891, when a significant workforce was relocated to Siberia to build the railway.
One would say that the first real attempt to populate Siberia was Stolypin reforms and resettlement program, so yes - only in the beginning of XXc did Russia put an effort on the official level to populate Siberia.