V-Flyer

I will be in BOS this year visiting family and whilst there we are taking a trip to Charleston.
I wanted to use Virgin points for the flights but could only find availability one way so booked economy with points and picked our seats. I could then see the flights on my VSApp and also on my Delta App.
We then decided to upgrade to First Class but couldn’t do it through VS so completed it on the DL App.
My upgraded flight is showing on both Apps - although my new seats aren’t showing on the VS one and my question is, Do I check in on the VS App or the DL one or does it matter?
Thanks

You always check-in using the carrier you are actually flying on. In your case that will be DL. Once you have checked in online or via the app with DL, your VS app may well issue a boarding passes as well.

I often find with VS+DL multi-leg bookings, once you have checked in online using the carrier you are flying on, the other app with then issues boarding passes as well.

When I flew to HNL last year which was booked using AF, flying VS+DL, all 3 AF, VS & DL apps actually issued my boarding passes for all flights!

Thank you James