So long as you keep the two itineraries separate -- under two separate PNRs, I don't think there is anything wrong with it.

If it's oneworld Explorer, the first sector is fixed and for the rest, if you have made reservations with AA or any oneworld partner airlines, you can just cancel all the reservations and ask your travel agent to rebook for all the rest of the flights under booking code A. This is what I usually do. I take control of all the sectors except the first. The rest I make reservations on my own.

I also have two Explorers and reservations for both were made almost at the same time. When I made res. for the second one, AA noticed that I have another reservation but this was because one of the sectors' dates (not the route) overlapped, apparently.