A couple of things:
As others have stated, a sealed box should have no leaks.
You should always have a good flat, secure mounting for your woofer. This will prevent frame tweak too. You wrote one of them sticks out a little. If the woofer won't drop in (A little snug is okay) the hole is not the right size. Correct that and please DO NOT force the woofer in by driving the screws in to try and "make" it fit. It can affect performance and sound. (suspension and cone movement won't be linear)
Is the enclosure the right size for the woofer? (Internal volume, etc. based on ratings of woofer.)
Is the woofer the right kind for the enclosure? (Designed for the enclosure you have. Ported, sealed, large, small enclosure)
The phase switch is there to reverse polarity of the sub. So it moves in or out of phase. Correct the speaker mounting and enclosure stuff first and then select the phase switch position that sounds best. Here's a small article from Crutchfield that may help. Tuning Up Your Car's Audio System
Tip: polyester fill can "give" you some "volume" in a sealed enclosure if it's a smallish enclosure or tight behind the magnet. Too small an enclosure sounds like poop too.