This is how I would do it. I will use FPCPP as the IWGP of this example.
Let's say we have 15 Feds in the Alliance and each fed would have their own WORLD or MAIN Champion. Let's say from JAN - OCT of the year, each fed are free to determine whoever their champion is / are. NOV would be end of the season for all the feds and all the champions, 15 champions representing their own fed, are entered into a play off scenario where all the champions will compete against each other where the winner will be crown the FPCPP / IWGP Champions, the champion of champions. This title and champion will be recognised all through the year or until he loses his fed's title which also forces him to relinquish the FPCPP title as the main rule / gimmick of the title is it can only be held by a champion.
During JAN-OCT period we could also have some special in season tournament and give the winner some #1 contendership for the FPCPP / IWGP title or a Money in the bank type of deal. This tournament winner will face the FPCPP / IWGP champion for not only the FPCPP / IWGP title, it will also be for the fed's title.
The idea is for all the feds be connected by the alliance and have this competitive spirit between the feds and yet are still free to do their own thing without worrying about this FPCPP / IWGP alliance.