I moved your topic because we have a separate subforum for audio questions.
I have installed many 3 way component systems in the past and I think you're going to have a really hard time getting them in the Element unless you do some custom modification of the door or kick panels.
6.5" woofers fit in the stock location (barely) with simple modifications like widening the opening a little and using metal clips for the speaker holes etc., even then, you have to be somewhat careful about how deep and conically wide the speaker you'll be mounting is because the window stops just above the speaker.
Assuming you wanted to mount the 4" mid right above the woofer, the window (when rolled down) will even more severely limit the mounting depth of the mid - it's probably not even be possible.
So... I'd suggest that you consider building some fiberglass speaker pods or having a qualified custom car audio shop do it for you. Another member (X2E) recently had this done with really nice results. A picture and the link to the post is below...
I know there's a woofer and a tweeter in that picture above so I'd suggest you use the stock tweeter location on the widshield post for your tweeter and use the pod on the door for your woofer and mid. If they are built out enough, depth shouldn't be a concern and as an added bonus, you can angle the speakers optimally and also seal off the back of the pod cavities which will help them sound their best.