In general, Perl will choose the right malloc for your system. I played around with these setting a couple of years ago and never saw any real benefit in terms of memory savings.

What's probably happening is that you have some data which isn't properly scoped so it's not getting cleaned up. If you can post some of your code, people here may be able to help. Make sure your are using strict and warnings to catch accidents.

If you have really huge data structures that you have to process, you could look for a way to swap speed for memory consumption by storing parts of it on disk while you work on it. (Storable is good for this.) Obviously this doesn't work with an approach that requires one large structure.