Secondary Fermentation

So I transferred my beer from the primary fermentor two days ago. While it was in the primary fermentor it had stopped bubbling, but I let it sit in there for two weeks just to be sure.

Transferred it to the secondary fermentor and now it is bubbling again with the dead yeast piling up on the bottom. I also added some hops to dry hop it after I put it in the secondary. So my questions are:

1. Should I pull out the hops now or just leave them in there?
2. Will I need to transfer it again to another carboy to get it away from the dead yeast to allow it to age?

1. No - leave them in there
2. No - unless you were planning on aging for months and months

I assume you did not take any gravity readings before transferring? It is possible it wasn't done yet (though at 2 weeks, I too would have expected it to be done). Could have been a stuck ferment that you kick started again by racking. Could be just CO2 off gassing from the racking or an increased temperature (is there a temp difference between now and then?) In any case, I'm sure it is fine. Continue with the dry hop as planned, but be sure to check the gravity and make sure it is stable before bottling.