The documentation in ExtUtils::MakeMaker says
"setting LIB overrides any setting of INSTALLPRIVLIB, INSTALLARCHLIB,INSTALLSITELIB, INSTALLSITEARCH (and they are not affected by PREFIX)"
This probably explains why your PREFIX declaration seemed to have no effect.
(I've usually set PREFIX and LIB to the same thing, and that seemed to work well. I remember noticing that if I only set one of them (PREFIX is recommended in many sources), I then had some problems. The explanations in MakeMaker have always seemed a bit cryptic to me.)
chas
(Update: I realized after I responded that you seemed to be asking about ExtUtils::ModuleMaker since that's what you are using...I don't have that and haven't ever used it.)