Hello! I have been a GM off and on for years but my current game is actually my longest stretch at it. I don't consider myself a bad GM - and my players seem to be having fun - but there is always room for improvement.
I have a busy job so I can't always spend a ton of time on game planning, but the group and I have invested a significant amount of time and effort in a custom campaign with elaborate back plots that I don't want to drop. I'm not terrible at making up encounters and fights on the fly (apparently, one - a shipboard fight on a mist-shrouded sea with scrags in the water like sharks - had some of my players talking about it the whole drive home. But one thing I always seem to forget is adding treasure later to make up for the less than ideal looting situations, which leaves my party a bit short on items.
Another issue is encounter balance. I have given them fights which go way over their CR and yet are too easy; I have also done fights which should be tough but doable and yet severely messed them up. For example: a dozen zombies should be a CR 6 encounter, which should be a pretty epic fight for an APL 3 party. Yet the players just about always hit the zombies, the zombies just about always miss the party, and so the fight takes a bit longer but still doesn't really trip the party up. A later similar fight against many more zombies was the same. On the other hand, a single Penanggalen using the stats right out of Bestiary 3 would have been about the same CR. (I added 1 because they were fighting it at night - and had no option of doing so during the day.) Yet here, even when I didn't have it using most spells and spell like abilities that it possessed (I think it only cast Obscuring Mist early on and used only physical abilities after that), I had to handwave things to avoid a TPK. To be fair, they had made some mistakes of their own - like failing to buy silver weapons even after making the knowledge check to know what they were dealing with - but often even hitting the thing was an issue.
So I guess what I'm looking for is a) any tips on organization that will help me keep track of wealth - or everything else - better so I can reward my party appropriately without them waiting forever between treasures and b) suggestions on encounter design that will help me keep things balanced when the CR system fails.
I appreciate any help on this!
The treasure issue could be solved by using the auto bonus progression out of pathfinder unchained. Personally I much prefer this system to the standard system. The game is written with the idea that you will have certain items at the appropriate level. The big problem is this means that the vast majority of magic items never get used. No one bothers with a cloak of elven kind because they need the cloak slot for the cloak of protection. With your wealth by level should be about half of what is listed, but any magic items become interesting instead of standard gear.
Another thing you could also do is have the party be part of an organization that fund and equips them. As they rise up in the ranks (gain levels) they are given progressively better equipment. This also solves the problem of the characters that by concept should not be worrying about treasure. The greedy thief is a classic concept, but the greedy paladin just seems wrong.