To the initial post:
at this point, I have two perfectly running instances of Cubecart v6 on the same domain, same machine, and same fix IP. Both instances work absolutely fine. One is in a folder of the main domain and the other on a sub-domain.
My hosting is a shared one at interserver.net on a Linux machine running Apache. So, I have no idea if it would work the same on a Windows machine, on asp.
Thank you Bsmither for the insights, especially regarding the usage of a common database and of sub-domains! I tried running both instances simultaneously using the same database but it is indeed prone to errors of input/output, as Bsmither was pointing out, if not handled with caution. For example, when clearing the cache of one instance while the other instance is still writing on the database.
Thank you Havenswift-hosting for the suggestion of using different skins for the two front-ends (wholesale and retail), as well! The reason I finally decided to run two instances of Cubecart is that in the near future the retail will be moved on a separate dedicated server and it will be much easier to just transfer the entire data than if having to first separate the wholesale data from the retail data in a common database.
To conclude: everything runs smoothly