you sound like you have problems accessing the files no matter where you place them, and not with where exactely to put them. I do not know about netbeans... but if you are having difficulties with accessing your files, first thing that comes to mind is that you have paths hard coded and that inside quotes, your backsalsh are very likely not correctly typed in.... they should be doubled... example:
"c:\mycomp\myfolder\myfile...." <-- see, double slashes :)