1968 350 HO, both heads have the small square hole in the center of the heads which face the intake. The manifold is a 9790140 which had a small hole in the driver side of the intake, facing the head (exact match to head). The pass side of the intake has a large/rectangle hole face a small hole on the head.
Which intake gaskets should I use? The driver side gasket's small hole slightly covers the top of the small holes of intake and head. Should I modify the gasket?
Like Q said, not a big issue, in fact when people swap out the original intake for an after market intake, or for many various reasons they block this port off. So either way as suggested, you will be just fine.
This actually happened to me. I thought it would not be an issue but I started getting an exhaust leak because the gasket was not corrected seated to match to ports. When I did buy a gasket kit it came with a cut out to insert into the smaller port hole of the gasket... BUT I may be wrong
It also depends on the heads. They changed the design slightly in some. The 6X-8's I have on my 455 right now this chamber is not open to actual the exhaust ports, so I didn't have to block it off and with the Edelbrock intake the top 1/4" of the opening is showing and open with out any issues... so you may or may not have issues if it's not blocked off properly depending on your configuration. Best bet is as Merv suggests and get the Felpro gasket set.