Its hard to imagine your exact setup. First, block all vacuum lines and run the motor like that, using only one line to your MAP sensor, and one big line to your ISCV if you use that. The motor should run ok. Then connect the booster up to either side you want (any ports not used have to be blocked). If the engine runs different with the booster connected you either have a leak in the hose, a leak in the booster, or your one-way valve is hooked up back-to-front. A healthy booster does not leak much air, even when the brakes are used, so don't worry about that. The stock 20v setup has a balance tube anyway.
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