so i have decided to go with a setup that would have a set of Rainbow 3-way components up front, which i believe would eliminate my need for rear speakers. so the question at hand is, when i remove the rear speakers would i be better off leaving the speaker holes open or closing them up?

the car is a 99 Altima, the rear speakers are 6.5" and the setup in the trunk is a SSA XCON 18 in a 5.4 cu ft sealed enclosure.

I left mine, make sure you deaden it all, it'll allow some air flow from the trunk to the cabin.

would it make a difference in opening the hole completely up and leaving the grill and carpet on the rear deck?

leave all that on, just take the speakers out.

I'm not familiar with the rear deck of a '99 Altima. In one of my prior installs in an older car I owned at the time, the fabric and cardboard material of the rear deck covered the speaker holes for the rear speakers (the cardboard was perforated). Removing the material from covering the speaker hole made a significant difference. To keep it from looking hideous I just used some old 6x9 mesh grills that I had.