Flooding bottom coil Phoenixes happen because: (in no specific order and probably not a complete list)
1. The top rubber seal isn't sitting far enough down or is otherwise not in there right. It could even be upside down.
2. Too much air in the syringe.
3. The middle post is raised too high and is letting too much juice through the holes.
4. The wicks are thinned out too much.
5. It wasn't filled properly. Perhaps it was filled too much (I always stop at the point where the middle post widens), wasn't filled upside down, there was still juice by the wicks when you refilled it. Pushing new juice in just pushes that juice through the coil and you'll start the tank with it already flooded.
If I get flooding and it's because I screwed up when refilling it, this is what I do. Wrap a paper towel around the threaded end and turn the Phoenix upside down like you would if you're filling it but leave the drip tip on. Blow through the drip tip until it sounds cleared out, cleaning up the juice that comes out with the paper towel. You do this upside down because otherwise you're just flooding it worse. You'll want to clear out the juice from the base that might be stuck around the wicks before you do this for the same reason. Just hold it by the threaded end and flick it a few times like a thermometer.
If it floods anyway, take it all apart and put it back together. Be careful to make sure everything's sitting properly. You'll want the post to sit flush against the cup surrounding the coil. The rubber seal needs to be right up against the rim on the post that it sits on. You should be able to see the metal of the post if you look down at the seal. This wouldn't help with dry hits, but it should cover most of the bases for flooding.
Careful taking the needle out after you fill it. Take it straight out and not at an angle. It can tug the rubber seal loose.
A few really small bubbles in the syringe isn't a big deal, but you just kind of have to get a feel for how much it'll tolerate. When I load up my syringe, I clean off the tip and hold it from there then flick it like a thermometer. It helps get the bubbles to the top quicker than tapping the tube or whatever you call it. Try not to stab yourself! Then, so I don't waste juice, I put the tip of the needle into the very top of the juice cap. I have those bottles with the round childproof lids. Holding the syringe with the needle straight up and against the tip of the cap, I depress the syringe until the bubbles come out. The tip of the cap actually holds onto the juice even though it's upside down. Then, I just flip it over, suck out the tiny bits of juice and load it up. Works every time!