Here's what I suggest:

Somewhere in you apache config file, add something like this (the exact path can vary, of course):

PerlRequire /var/www/perl/startup.pl
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Then create startup.pl so that it looks like this:

use lib qw(/path/to/my/modules);

use MY::MODULE;

1;
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The use lib line adds directories to the search path. If you actually put use MY::MODULE in the startup file, these modules will be preloaded when apache starts up.