Well, in regards of prana - It doesn't seem like everyone are able to utilize it. Either that, or they are able to, they just don't use it. Saber (Arthuria) uses it commonly, while a lot of other servants don't tend to use it at all. Caster is the main exception to this since he is the only class that can supplement himself with mana, and therefor can in theory live without a master to keep him present.
In the last episode of the first season of Fate/Zero, when Arthuria uses her Noble Phantasm, yellow orbs started to flow towards her, which Irisviel referred to as "The wishes of fallen warriors" or something among those lines. Now, this is just a theory, but I would therefor assume that Prana comes from the souls of dead people? It makes sense in my head at least Regardless, that would also explain why we didn't see any of the same orbs when Arthuria used Excalibur for the second time, since they were inside a building, unlike the first, when they were outside. I don't think we ever got to see Arthuria using the Prana Burst ability when she was inside a building either.
I use the Type-Moon Wiki
as my source. ^^; It's compiled based on information in the games, books, and statements made by the authors, so it's generally considered fairly accurate. The link I listed goes to the entry on Prana, and gives both a basic overview on how it's supposed to work, along with some hard numbers at the bottom. I'd especially like to point out the numbers given for various activities by Saber at the very bottom.
Basically, when it comes to supporting the existence of a Servant, two things are needed. The contract with a Master is necessary to provide an anchor tying the Servant's spirit to reality, and then there's an upkeep cost in Prana that's needed to counteract the effects of the world itself trying to erase the Servant from existence, because they're already dead and thus shouldn't be up and walking around. Anything that would require the Servant to expend energy (such as fighting) can increase this cost, and anything that would cut down on the Servant's energy expenditure (such as sleeping, or going into spirit form) would similarly decrease the cost. Naturally, activating a Noble Phantasm will generally require a huge expenditure of Prana in order to support its miraculous effects.
Overall, though, I wouldn't worry too much about tracking Prana usage. I think the general assumption being made is that the Masters in this game are all competent Magi, and so you can stick to a more narrative take, with regular fighting being easy to handle, and only the big, flashy stuff really requiring Master and Servant to spend some time recovering.