i bought a new edelbrock intake manifold for a 360 sb and on the heads there are the water jacket that flows through the stock manifold but this intake does not have the water jacket when i just set the intake on the engine the hole in the heads go over the edge of the intake by about 3/4 of a inch is there some sort of block off or what do i do.  

Sounds like you have the wrong intake for your engine . Is the 360 you have a LA engine or Magnum engine. It sounds like you have LA engine and a magnum intake. LA engines were made from 1967 to  1991,Magnum engines were made from 1992 on up. the heads and intake are configured different.  

There is what looks like a gap between where the intake sits and the cross over don't let that fool you the actual passage is smaller than that.

Hopefully you didn't end up with a narrow pos chvy int.

The rear water cross over/cooling passages don't cross through the intake, just the front ones. Don't get confused with the heat cross over, or on early truck motors, the water heated manifold which uses the exh/heat cross over in the manifold AND special heads that do not intersect with the exhaust ports [for obvious reasons]. .

SO, if you have these heads, #234 T-318, and don't want hot water under your carb or in your EGR VALVE  [if you were to have one] then you just block them with a piece of thin sheet metal and some RTV.