Mod folder?

ok, since im making such massive changes to rtw, i am wondering how to go about making a mod folder. ive looked in the scriptorium and i didnt find anything informative. could somebody explain how they work, and how i can go about making one. the things i really want to know are if the mod folder will run through the BI engine, whether i have to set all of the pak files in their proper places if i want new faction symbols, and if it is essentially the data folder with your modded files?????
i would really appreciate a detailed answer....:laugh4:

lastly i noticed the bigger mods come zipped, how can i go about this to minimize the space of the folder, i have to transfer in to a new computer soon, via a 1gb usb drive i have about 400-450 mb free

oh yeah, i found in the scriptorium a toturial on geographically accurate maps. does the tutorial still apply/work?
thanks for the help!