The system allows you to add an unlimited number of eBay accounts. You can add additional accounts by going to ebay > setup > store manager > Add New eBay Account / Store
After you add another ebay account you will have to generate a token for it by drilling into the ebay store from store manager page and clicking Generate New eBay Token
To remove and eBay account that has no templates, transactions or orders associated with it you go to eBay > Setup > Settings > Store Manager > select account > click delete selected.
To remove an eBay account with listngs and/or orders please check guide here.