There's no issue in using the sealant in the manner you are prescribing. Sometimes you need something to hold it in place. When you do so, the side with the sealant is most likely ... well ... sealed. Something to look out for is to ensure your coverage of the sealant is fairly even. If you get larger "lumps" or sealant in areas, it won't allow the gasket to form tightly on the non-sealant side and can cause leaks. Also, you'll do better if you can put your gasket in place sooner rather than later after application of the sealant. You aren't really using the sealant for its sealing properties, but rather for its stickiness. If you wait until it is partially cured, it's easier to run into the unevenness I was talking about before. Get the goop on there, place your gasket, then place the gasket and cover (whatever piece you're sticking the gasket to) into place, torquing when appropriate. Don't hesitate, just get it done.
Most newer engines have captured gaskets with metal reinforcement which holds them in place fairly well. You shouldn't need nor really use sealant on these types of gaskets. While I don't have any proof, it is my belief you'll run into all kinds of sealing issues if you do.
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