Approach 1: Have a main script (e.g. main.fcgi) that distributes work to modules

#!/usr/local/bin/perl -T

use Module1;
use Module2;
use Module3;
code to initialise variables

while (my $q = new CGI::Fast) {
    code to distribute job to Module1, Module2 or Module3
}

Approach 2: Three FastCGI-aware scripts named module1.fcgi (functionally equivalent to Module1), module2.fcgi (functionally equivalent to Module2) and module3.fcgi (functionally equivalent to Module3). Each of these scripts have more or less the same structure:

#!/usr/local/bin/perl -T

code to initialise variables

while (my $q = new CGI::Fast) {
    code to run 
}