You should not run different versions of perl. You (everyone) should keep your software updated and current.

Having two versions installed is not so uncommon, actually, e.g. the Perl that came with the system, plus another up-to-date one for your own use. In fact, I'd think leaving the system Perl alone is a much better idea than forcing some newer, but slightly incompatible version upon all the system tools that use Perl — just to always have nothing but the newest and shiniest... (In particular, on Solaris boxen, where the system Perl is often rather ancient, I'd rather not mess with it.)

Just keep the different versions under different installation paths, and with a bit of care and awareness of the situation, everything should be fine.  I usually have two to four perls installed on one system (e.g. 5.8.8 (system perl), 5.10.0 (to stay up-to-date), and one or two other versions (including an old 5.6.1) for compatibility testing etc.). Never really had much problems with it, except when unconditionally setting PERL5LIB.