Battery3:I have created lots of kits that were all originally derived from a few built-in presets. Whenever I add drums to a project I use an existing kit (plus associated drum map) from another project and modify it further. Then I save it for reuse.
DimPro, Rapture:I normally find a preset that is near to what I'm seeking and tweak it. Sometimes I remove one of the elements or add a further element. Usually I alter the envelopes and LFOs.
Z3ta+ (1 & 2):I tend to stick with an existing preset. Any changes that I try to make usually ends up sounding worse.
Other softsynths:I generally find an appropriate preset and tweak the settings.
Reverbs:I usually find a suitable preset and modify the timings and EQ.
Delays, Compressors, Gates, EQs, etc.:I rarely use presets with these.
Sometimes I save my own softsynth or fx settings as a preset for reuse. When I do, I save it within the project folder itself, in a sub-folder called "Settings". Of course, if I want to use it again in a later project, I will need to remember in which project I first used it first. Usually I do remember. I don't save Battery3 kits there though.