This is entirely possible, I avoided using them for about a year and a half becuase it shit me that I need to add them to my mission folders, I now have a seperate scripts mod folder and when I find a script that is finished and only the parameters of it's exec line need changing I then pbo it and add it to my 'script mod folder'. This folder contains scripts for blizzards/snow&sandstorms/paradrops/toxic areas etc.
If you have a scipt called name.sqs, add it to a folder called, say, folder. Pbo it into folder.pbo and put it in an addon directory/mod folder. and exec it with.
[] exec "\folder\name.sqs"
I hope that makes sense. :-\
Captain