Acrylic cutting requires just the right speed -- too slow and it "grabs" too fast and it melts. I find it best to use a fast blade and move it through the material fast so the hot blade doesn't stay in contact at one point long enough to melt it.
Polycarbonate (Lexan) is a little more tolerant and easier to cut. It's also very easy to bend and doesn't crack as easily. IMHO not as good for a clear water tank top because it will flex and bend when the water sloshes (or it it's leaned-on at one point -- especially if it's under a berth).
Also (for other applications) Acrylic stands up to UV much better.