Absolutely - in fact, you can configure where pull requests from collaborators go and where pull requests from non-collaborators go by going to Project Settings->Columns.
If you reference an issue number in a pull request title or pull request body using GitHub's issue closing keywords, those issue(s) will move to the column of your choice once the PR is issued. Note that if you do not use GitHub's issue closing keywords and instead use Waffle's "Connect" keywords, we will move that issue into your "In Progress Start" column (set to "In Progress" by default.)
From the Project Settings->Columns screen, use the colored bars for “New Collaborator PRs” and “New Contributor PRs” to configure where pull requests are shown when they are initially opened.
Read more details on configuring which columns your pull requests go to on our blog.