That's weird, she should have done more than take down your email and give you the store link, she should have handed you an application to fill out on the spot, then you should have handed it back to her after taking some time to sit down and fill it out like fifteen minutes later. You should also carry around with you copies of your resume into every store you go to, so that when you hand them back the application you hand them your resume along with it. Stay away from the online application because you're right, you will get lost in the database.

Yes I would email her back. I don't think it matters when, but I would do it ASAP so that she knows you're really persistent. Also, if you can, go back to that store and ask for an actual application. If she asks why, say the link she gave you took you to the store's national online application for all of Ohio or whatever that was about.