Well, the computer radio's settings won't be affected, but they won't be in effect either. On most buddy box setups, all control is switched, it's as if you turned off one transmitter and turned on the other in the air. So if you set lower rates and expo and subtrims on a computer master, none of that will show up for the buddy box. This is usually backwards of what you'd want. So except in special cases, when you set up a trainer with a computer radio and a non-computer buddy box, you want to turn off all the rates, expo, subtrims, etc. everything to 0 or 100%. Then set up the plane the old fashion way, by adjusting the linkages on the airplane itself.

(one thing you can do is set the computer radio EPA to something higher than 100%, this gives the instructor more throw than the buddy box, which is useful).

Oh, if the plane has been trimmed out and flys straight and level hands off on the master, then you can trim the buddy box by making sure that nothing moves when you flip the switch back and forth. Do it at center to check the trim settings, then do it while holding both the master and buddy box sticks at full throw to make sure the buddy box doesn't have more throw than the master.