Getting call options such as skype/viber again
The option to choose what application to use when making a call (or anything else, such as open a webpage) happens when you don't have a default set. So if you want to get asked whether to use Dialler/Skype/Viber when you try to call a contact, then you need to clear the default settings for Dialler. You won't get the prompt otherwise.

There is no way to set this up on a per-number or per-contact basis in the Dialler.