Ally, I found myself in a similar position. I had a few ideas, characters, a beginning and something of an ending, etc, but no idea what to do in the middle of all that. I found the 7-point Story Structure idea useful in preparing. By backing off and focusing on the bare-bones, I was able to figure out the basics of what I wanted, then going through again I could flesh it out a bit.

Here's the link Brandi provided: http://www.writingexcuses.com/2012/10/07/writing-excuses-7-41-seven-point-story-...

And here's a powerpoint (it will download if you click on the link, so be aware) that went into depth and I found very helpful: www.monkeysloth.net/fearful/StoryStructure.ppt

You can use it to figure out your main plot AND subplots, flesh them out, then figure out how to fit them together.