The shebang line (#!) is used to giva a path to the perl interpreter.
On a windows system, this means all your perl scripts must start with #!c:\blah\blah\usr\bin\perl.exe
and before you upload to your unix box (or web server) you need to change this to #!\usr\bin\perl
If you have a good text editor that can do a replace on multiple files, this is pretty easy.
If you put perl in your apache folder and configure the sub-directories to match your server.
Example:
On you server the path to perl is \usr\bin\perl
so on your computer you would need to place the perl executable in c:\blah\blah\apache\usr\bin\perl
Then you can use the same #! line for both. On the web server, it's an absolute path, and on your comp it's a relative path, but they both work the same!