when you are in admin and click the modules/ceon uri mapping (seo) config/installation check

that last one will give you a linksaying "click here to go to......installation check page, it will then check to make sure you did it right, then at the bottom---if no errors pop up---you wil see the code to put into your main .htaccess file.

If you do the same thing for your wholesale store and the code is different then you can just add both codes to the main .htaccess file

making it a subdomain in your c-panel will actually make it appear as though it is a "real" domain vs an extension of the main store.

You will most likely need to edit your two config files with the proper path information. The store links will be different also so you might need to reset those also. It has been awhile since I set up a sub domain so my thought process is rusty.