Assuming you have bought a current version of VS (rather than VS6) then you will be using a .Net language for development. VB.Net is fairly different from VB6 or VBA although there are similarities in some of the syntax, especially if programming against an Office app.
How difficult it is to convert an Excel app to a standalone app will depend on how much of the native Excel functionality you use and therefore need to recreate.
I would say it certainly won't do you any harm to learn a .Net language, as Office will become more orientated towards it over time. That's not to say that VBA is going anywhere any time soon though!