Haskell mode doesn't seem to be resolving the modules in emacs when I use the stack command to build my project.
Is there a file that I have to edit to tell haskell-mode where to find the packages that stack installs from stackage?
All you (should) need to do is insert the following line in your emacs config:
(setq haskell-process-type 'stack-ghci)
That tells emacs that you want to use stack's repl command instead of whatever haskell-mode tries to infer automatically for you.