If I understand the OP correctly, it sounds like he has one of the WMS catch cans -- the top fitting is for your breather/filter, the side fitting is for your inlet line coming from the engine, the bottom hole is for the petcock / drain valve.
If there are additional fittings on the catch can, either plug them, or install additional filters on them. IF you have one of the older (oversized) catch cans, OR have one with PLENTY of ventilation, I'd have no problem venting the carb overflow tube to the same catch can as the valve cover breather -- BUT, if there's any doubt whatsoever, simply use two catch cans. You can use this to help diagnose a problem as well (ie sticking carb inlet needle will fill a catch can in no time.)
ALWAYS use a clean filter on your catch can to keep harmful dirt from getting back into your engine.
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Thanks and God bless,
Brian Carlson
Carlson Racing Engines
Vector Cuts
www.CarlsonMotorsports.com
765-339-4407
bcarlson@CarlsonMotorsports.com