no limits

I have a newer Hardin marine sea strainer. It is roughly 9 1/2 inches tall w/4-1" npt ports (2 in and 2 out). It also has 2-3/4 inch npt ports on the side. Has half the ports above the grill (as I call it) and half below. As far as the main plumbing, does it matter if I go in above the "grill" and out above, or in below and out above or whatever? Also, should I use one of the 3/4" ports and run a line out the side of the boat to blow water out to relieve pressure or not? Help please and thanks!