I'm sure there are many opinions out there, so don't just run with mine, but here's my suggestion:
Add a restricted access network folder (a folder on your network to which only you and your crew have write-access, but everyone can read) to the top of the Support File Search Path list. (ex. S:\CAD\Support)
Copy all your files into that folder.
Create files in that folder called "acad.lsp" and "acaddoc.lsp"
The acad.lsp file will run every time the program is initiated. (Figure maybe once per day)
The acaddoc.lsp file will run everytime your users open a dwg. (Multiple times per session, even read-only)
Figure out which routines need to load with which file. (You may not need both, depending on your situation)
Cross your fingers and hope all your routines work (or you'll hear about it loudly, clearly, quickly and repeatedly)