If this is ingame you can easy use all the seven without the needing of make substitution.
Just rotate the strongest Pokemon for the weakest every time you reach the Pokemon center, you don't have to limit yourself with only six Pokemon.
Last time I was in Gen 3, my ingame team was made up of 10 Pokemon, Gen 5 was 13 Pokemon, and Gen 6 was 22 Pokemon. They were never underleveled.
If you not aquaited with training many at the same time, just add one more instead of many at the same time, for example, if you have the team of six, just add one more and make a team of seven. You'l have fun having the seven Pokemon you like and they will not been underleveled.