I'm pretty sure there isn't a way to use IM to do the applying since everything is already posted. I'm not sure about Smart Connect.
You could use a macro in the Apply Payables Documents window. First you'd need to get a listing of all the payments and/or other credit documents. Then build a macro with mail merge (see here: blogs.msdn.com/.../how-to-use-word-mail-merge-and-macros-to-import-data.aspx).
Essentially you'd have to rely on the Auto-Apply button which would be based on Document Date or Due Date depending on how you have the module setup. I'd test this out on a few documents first to see if you are getting the expected results.