Difficult to comment without knowing what one of your .conf files looks like. One possibility is to use 'do' rather than 'require', and import each one into a different namespace. For example:

/tmp/foo.conf:

    sub f { print __PACKAGE__, "\n" }
    1;

main script:

    package P1;
    do '/tmp/foo.conf';
    package P2;
    do '/tmp/foo.conf';
    P1::f();
    P2::f();

which outputs:

    P1
    P2
[download]

Dave.