I think that Dipper is actually being manipulated by Bill, but not in the way that you think.
He made a deal with Bill, but remember, that deal was never terminated. Bill technically still owes Dipper a favor, but he's puppeteering Dipper from outside the dimension. He's making Dipper paranoid, feeding him small bits of information through his dreams.
Art Credit to boomsheika.deviantart.com
Dipper can't sleep anymore, and he doesn't want to sleep, because he knows Bill will be there. Then again, he does want to go to sleep because he'll get more information. He's being conflicted, but Bill isn't possessing him, he's using simple mind tricks to make Dipper lose his mind.
Even without Bill's help, Dipper was already almost driven mad at the mysteries of the town, even though making progress. He now realizes that he's getting information, but it's very small. Something so tiny that he knows that there's something bigger, but he doesn't have enough to piece together. He's now following the human "completion principle" where he needs to know more.
Dipper is being weakened by Bill. Bill realizes that it doesn't matter how much Dipper knows, when he's weak enough, Bill could take Dipper's body to use as a physical form.
Yet, in the upcoming episode "Weirdmageddon", it seems that Bill has bridged the Mindscape and the real world, allowing him to be in the real world without a form. I don't know how this will work, but this is my theory!