We actually an \"extension\" or solution to help you with multi-channel cases like you are mentioning. Using the nChannel connector for Magento you can quickly and easily integrate and connect Magento to a variety of POS, ERP and accounting systems. For existing Magento sites, once downloaded, our Magento connector starts copying your customer, item, sales and supplier data to the nchannel platform. Simply add additional connectors for the other channel systems you use to begin exchanging data between Magento and any other channel.
This is great for multi-stores and channels as it helps with order management, inventory synchronization and customer data integration:
The simplest way (and most used) is to give the two stores the store codes “retail” and “wholesale”. This is done in the admin menu System > Manage Stores.
Then, in System > Configuration > Web > URL Options, change Add Store Code to URLs to “Yes”.
Since the two stores have separate products, and probably separate customers too then it makes more sense to have them on two separate websites too. Even though they are called “websites” in System > Manage Stores they do not have to have different domains. It will still work perfectly well.