I've heard a fair amount about the Hussite military and its leadership, but I really don't understand how Bohemia was governed overall during the Hussite Wars.
Was it a sort of military dictatorship, with generals like Zizka and Prokop having the authority to appoint and dismiss civil magistrates, issue edicts, etc?
Was it ruled by some sort of pro-Hussite rump of Bohemian nobility, with pro-Catholic nobles having their feifs seized, and their titles granted to the second sons of favored pro-Hus nobles?
Did urban communal governments with patriciate-elected councils have a lot of influence beyond their city limits?
Was it a theocracy? Did the Hussite church have a lot of voice in government?
None of the above?
Was there a clear overall leader of Bohemia, beyond the general responsible for fighting battles against crusaders?
(N.B. This is a repost.)
I will try to answer this at least briefly as it is quite deep question and there are no answers yet. I have to apologise I will quote sources in Czech language as it would be difficult to search for it in English.
First of all your question suggest existence of one government which is not correct. The reality was a mixture of smaller units which differed due to regional and political conditions. First of all there was short and intense religional dictatorship of Jan Želivský 1419-1422 mainly in New Town of Prague (simplified explanation).
Beside this we can speak about 5 main fractions called mostly svaz (union):
Each of this union had slightly different approach and motivations which led to rivality and confontations interupted only under external threat (i.e. crusades) which made them to forget the rivality and to create miltary very strong army with well known victories. In such case it was Jan Žižka as an undoubted genial military leader who led the Hussites to the victory. Beside the period of threat and especially after Žižkas death there was a fight for dominancy between all unions and their leaders which led to the final defeat of radical Hussites in battle of Lipany in 1434.
Basic source is here, other sources are in related books:
Bartoš, František, Michálek: Husitská revoluce I. - II. České dějiny II/7 - II/8. Praha 1965 -
1966.
Čornej, Petr: Tajemství českých kronik. Praha 1987.
Čornej, Petr: Lipany. Slovo k historii č. 21. Praha 1991.
Čornej, Petr: Lipanská křiţovatka. Praha 1992.
Kejř, Jiří: Husité. Praha 1984.
Šmahel, František: Husitská revoluce I. - IV.. Praha 1995.
As I mentioned before I am sorry to not use English sources and also for my grammar mistakes.