I have compiled a few rules about using Handwavium in my settings.
1) Use handwavium only in the interests of expediting stories.
2) Use only as much handwavium as you need for the story. You pay for handwavium with your players' disbelief.
3) Figure out the fallout from your handwavium.
4) Put limits on your handwavium. Just because you're playing merry Hell with the laws of physics doesn't mean you should get cocky. It also keeps the handwavium from becoming the answer to all problems.
5) Be on the lookout for unobtainium that can replace the handwavium (more unobtainium is being dug up every day.)
Disclaimer. I am not a scientist or engineer. I have often gm'd scientists and engineers.