Once I have set the flight secuence on the Fmc and I am on route, will I have to rotate my CDI every time the course changes using the AP in nav mode or won’t it be necessary since the UNS is working?
It shouldn't be necessary to adjust the CDI at all as the FMS updates this for you on most equipment as it ties directly into an RMI. If you were flying an aircraft where you had to manually adjust the CDI, then having an FMS is overkill.
With that said, a limitation of the UNS-1 is that you cannot use it for final approach track guidance when flying a ground-based precision approach (i.e., ILS). So my previous statement about not adjusting the CDI is correct for all UNS FMS operations, except for final approach tracking of an ILS.
In that case, there are two options:
1) Without the UNS Enhanced Navigation package (typically up to the UNS-1C or D IIRC), you would have to change your nav source over to traditional methods when intercepting the final approach track. This would require that you change the CDI track to the inbound localizer. Setting the inbound track like this would normally be done in cruise and before or during the approach briefing. It depends on the installed equipment for just how you would do this.
I've flown aircraft where you had to change the flight director from LNAV to HDG SEL, then change the navigation source from FMS to LOC, and then input the inbound localizer track. You'd then change your navigation source back to FMS and reselect LNAV until such time you were ready to commence the approach where you'd do the same technique, just without inputting the track.
I've also flown aircraft where you did not need to modify the flight director, but you still had to change the navigation source in order to program the inbound localizer track.
2) With the UNS Enhanced Navigation package (typically UNS-1e and after), you have the option of having the FMS autotune the localizer for you, after which it will "ghost" the localizer until interception where it will automatically swap for you with no additional inputs. This is, by far, the easiest option, but it also requires a lot of integration with the aircraft radios, so I've only seen it where the FMS came as stock standard equipment from the aircraft manufacturer - think, Q400.