So what you're saying is, instead of stops at 6th and 8th Avenues, have them at 5th, 7th, and 9th Avenues? In that case, I'd locate the entrances and exits at these locations:
Lexington Av/50 St: at 3 and Lexington Avs (transfer to )
5 Av-Rockefeller Ctr: at 5 and Madison Avs
7 Av/50 St: at 6 and 7 Avs (transfer to )
9 Av: at 8 and 9 Avs (transfer to )