I'm a bit rusty these days, but here are some suggestions:
First, if you have Rptr, Gaming Evolved installed as part of your Catalyst installation, uninstall it. It causes problems with GameEx.
It's been a while for me on the system pack side of things, but I do recall that you must follow it through step by step exactly as it's outlined in order. It worked perfectly for me when I last installed it.
The paths do not matter, and if you let the system pack do its thing, then just follow whatever it defaults to. There is no guide I'm aware of for this, Tom simply created these for people who didn't want to hunt down artwork, snaps and the like. It is simply provided as a convenience for GameEx subscribers.
As Tom mentioned, your directories can be anything. C: \Chocalate\snaps, literally anything. As long as you point the setup wizard to them, it doesn't care, and what's in there by default are merely suggestions. If there are things in the wizard you don't have, skip them. It only uses the resources you direct it to use.
I run mostly GameEx proper, so in referring to that, ensure that you are running integrated mame.
This guide needs to be updated to come up to speed with the newer setup wizard, but this is the section.
Complete it through the "advance mame settings"
Don't confuse AdvanceMame with advance mame settings. You only need to worry with this section if you're running advancemame.
By using the integrated MAME support you need not work about any "MAME" stuff in the emulator section, your not running it as an emulator.
The integrated MAME support will do everything you need it to, assuming you've got your directories correct.
You should have to update each time you change something while using integrated MAME, but only upon a change.