My way for years has been to start with a good gasket, such as a Fel-Pro (doesn't have to be Fel-Pro, just avoid the bottom of the barrel parts store generics), and clean/chase the threads of the intake bolt holes to ensure they can be easily run down with fingers. Make sure your block and manifold are clean, and free of any major corrosion (especially with aluminum manifolds..major corrosion/pitting of the manifold can cause problems regardless of what gaskets or sealer you use).
Set the intake down without any gaskets or sealer in place, and finger tighten a couple bolts on either side. Check your distance between the block walls and front/rear of intake manifold. Barring any major milling of the intake/heads/block, this should be less than 1/4".
A thin film of RTV around the water jacket ports on both sides of the gasket, otherwise no sealers on the gaskets themselves. 1/4" bead of RTV on the front and rear walls, and just barely up on to the heads..kind of creating a "shelf support" for the gasket ends to sit on, and keep it aligned with the ports/bolt holes. Let it set up for 15 minutes or so. Set gaskets in place, making sure to have the bolt holes already lined up here (this is where that RTV "shelf" comes in handy)
Carefully set the intake straight down, avoiding as much movement as possible. Loosely seat the bolts down finger tight, and then walk away. Preferably for 24 hours (as this is the cure time of the RTV), but at least 8 hours/over night. This sets full contact across the block walls and the RTV, as well as between the RTV and manifold.
After the waiting period, come back and torque the intake bolts down to spec, in two stages - 20ft-lbs on round one, 30ft-lbs on round two. Fill 'er up with your coolant of choice, purge the air, and go!
Using this method, I've never had any gasket related leaks on a SBC or BBC intake. I've heard of guys using a ***** punch to "golf ball" the block walls and intake manifold, and I understand the thinking, but I've never needed to do it.