Umm..... Unless I'm missing something, Perl is only a unit frame addon. SCT is a scrolling text addon. Their uses do not overlap.
You can use many many mods all at once.
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"You'd be surprised how many people violate this simple principle every day of their lives and try to fit square pegs into round holes, ignoring the clear reality that Things Are As They Are." -Benjamin Hoff, The Tao of Pooh
If you use a premade UI package that has different unit frames from Perl (such as Xperl or ag_UnitFrames) they will overlap. However SCT and Perl will work together (as will SCT and other unit frame mod) and make a great combination. You easily tell WoW which unit frame mod to use (if you have multiple installed) via the AddOns screen.