Using either my suggestion or Jason's just allows you to make whatever adjustments you want to your store files in your local machine - i.e. template changes etc. - without affecting your overall site structure in any way while keeping the store structure intact.
Once you have the store looking as you want it in this local 'store' site, you can upload the whole folder (called 'store' or whatever) in to your remote site. All you need to do then is change a couple of paths in your hosting site database.
So your store could easily be at store/