I'm assuming you're asking this for online matches, although you didn't post in the correct forum (I'll move the topic soon).
So yup, skills are used in the online matches, in the same way than in matches against the CPU.
So, in Fair Play you have a max average of 75%, and in Tourney 50%.
No restriction in free mode, so it's better to have 100% everywhere.
Let's see Fair Play in detail.
If lag is >= 50ms, no strong serve, so max service skill will be 50%.
75 x 7 skills = 525 points to distribute.
So for a rally player a quite good setting would be :
Forehand, Backhand & Form at 100%.
Service at 50%.
Volley forehand & backhand at 60%, smash at 55%.
And if you just let them all at 100%, the game will lower them to 75% average by itself.
I'll let you find other good settings in Tourney mode, or with other play styles...