You're going to have a lot more runaways in the next few years. Why stay put in South Carolina when the slaves have been freed in North Carolina? And why would (for instance) a deputy in North Carolina care about sending slaves back over the border when they'll just be freed again in a year? Especially if all the escaped slaves want to do is head west.
This point is an exquisite combination of insightful and obvious -- I'm angry you thought of it first.
My guess is that Congress will establish the Freedmen's Bureau and pass the 13th Amendment before the 1864 elections in the hopes of dealing with these questions, but the early implementation will prove inadequate for the reasons you've laid out. So one of the big election issues will be how to run the Freedmen's Bureau.
Personally, I would vote for the candidate who proposes Sandman's idea:
One big idea: make "40 Acres and a Mule" a more general land reform instead of just dedicated to the freedmen. Giving the poor whites reason to identify with the poor blacks, splitting them from their dependency on the wealthy plantation owners, and generally putting the huge plantations to more productive use would be an excellent move both politically and economically.
But Sandman's idea might be a little too Communist to win the day. So perhaps the moderate solution is: (1) government subsidizes anyone, white or black, who takes to the frontier in a civilized manner, with certain free supplies (fruit tree seedlings, mules, a town hall), (2) fugitive slaves get "assumed manumission": if they state who their owner was, they are allowed to alight for the territories and their owner gets recompense, (3) the government auctions railroad rights to fund the project. My moderate solution has its own quirks, most principally that it will encourage a denser, less wild-west style expansion, so it's certainly not the only answer.