Another issue to consider when integrating third party shop software is the members' database will be different to the shop customer database so members will have to log on separately to the shop and vice versa.
If it was possible to merge both tables then you create another issue if selling physical goods, and that is you will need to collect addresses to post items to.
Much simpler to run the shop software in a subdomain or separate folder and link to it.
I modified the checkout side to inform users that they will need to register or check out as a guest if they hadn't used the shop before.