I'm a bit confused as to the query - but my understanding of the query maybe it helps.
Parent Pages are in Pairs
Side by Side in Parent Page layout they'll show A and A
If you want B
Then you have to apply Parent Page B to the page in the layout.
So if you're alternating page numbering colours throughout - then you need to apply Parent Page B to all pages that require it. Pretty sure you can multi select pages then Apply Parent Pages.
However, this is a very complex way - if it's every odd page numbering is a different colour. You only need 1 parent page - and in the Parent Pages set the text colour for the right hand side page to be Red text.
Now you only need 1 parent page.
If it's spread out across odd and even pages - then you'll need 2 parent pages and manually apply the correct Parent Page to the layout.
As pages add and delete etc you'll need to reapply the parent pages. So maybe do this at the end/final layout.
I always got the correct page numbers on my pages when putting in the page marker on both, but now I'm getting for example on pages 2 and 3 - both a '2'
You can get two number 2 pages or any way it's setup in the Numbering and Section Options - maybe this is what is going wrong for you.
It's hard to know - it would be great if you could supply a sample file so we can examine your setup and best guide you.
You can see the little triangle sitting on top of the page - that denotes a Numbering and Section marker - if you double click it you can edit the Numbering and Section option and turn off Start Section.
The parent page A will show a letter A, assuming you put in a Type > Insert Special Character > Marker > Current Page Number (Cmd/Ctrl+Opt/Alt+Shift+N).
If you have Facing Pages checked on in Document Setup, then both the left and right A-Parent page will show an A.
Then later, after double-clicking to a physical page in the Pages panel, you should see that A marker show a page number.