As fun as it is, in many regards the whole set-up of the Master league is kind of lame. I wanted to do the same type of thing you want, so this is what I did:
I made league A the "British Premiership," combining the current EPL teams with three Scottish teams (Celtic, Rangers, Hearts), putting the top 16 in D1 and the remaining 7 in D2, with my created team. I recommend creating/using a current Coca-Cola Championship team of your choice for the final spot (in my case I created Plymouth Argyle, with the help of the Coca-Cola Championship OF on this site by.... was it Paul_B? I forget...).
After that, I basically just combined the best teams from the other Western/Central European countries semi-geographically. For instance, I combined the best of La Liga with the good Portuguese teams, I put the best of the French teams with the best of Serie A, and I combined the best of the Bundesliga with the tops from Eridivisie, and through in a Belgian and Swiss team or something (which I called the Hanseatic League, because I'm just a history dork like that).