I'm not sure if your text was unintentionally misleading, but just to set the terminology straight for everyone, there's no "square polarizer" in the sense that there is a "circular polarizer". There, however, might be a square circular polarizer. As far as polarizers go, there are circular polarizers and then there are linear polarizers. I found a nice article about this topic on
http://www.photofilter.com/cir_lin.htmlBut to answer your question (a bit), at least the circular polarizer found in Cokin's filter system is a round one, that fits in the square filter slots.
As a curiosity, I tried to use my screw-in polarizer (mounted between the lens and the filter system) with Cokin's system and a ND grad, but it was more trouble than what it was worth as the polarizer rotated when I tried to align the horizon with the grad filter.