There are four skill sets.
Football skills: these are the bread and butter of a player. If they have no skill, they cannot play
Strength and conditioning: somewhat used to help with endurance, but mostly used to make the players fatter
Adaptability - use this if you plan on switching a player's position or playing him out of position (e.g you have 4 FB and 2 RB so you want to switch a FB to RB OR if you have multiple CB but 1 FS maybe you might end up having to play a CB at FS, then use this.)
Disclaimer: Academics is important as balls. A player is useless if he cannot stay on the field
Now, to set training, I look at things based on player position:
WR, QB, CB, FS, - these are positions in which skill is most paramount. I set most of my 100 pts for skill on these players. I put that based off of size and academic performance.
ex. WR Joe Blow: Ht. 6'3 Wt. 215/225 60 hands, 75 route running, 60 endurance 2.35 GPA
I would train him at (60 skills, 10 st. 30 ac). His skills are pretty high so I don't need to use all my points. a couple extra pounds would be good. Even though his GPA is over 2.0, it could take a nosedive and I need him on the field, so I devote a big chunk to that.
ex. CB Jack Black Ht. 6'1 Wt. 201/207 75 coverage. 70 tackle, 68 speed, 75 instincts, 50 jumping 3.1 GPA
I would train him at 100 sk. All my points would be used for his skillset because his GPA is fine and his weight is fine (I want WRs and DBs to be within 5 lbs of their target) so I devote it all to skills to hopefully improve his jumping.
Size is most important in these positions, esp. in the middle of the line (OG, C, DT) DTs need to be big so they can clog the middle and OG and C need to be big so they can push those big DTs out of the way. DEs are usually smaller than DT and OG/C is usually bigger than OT.
ex. (OG Jim Smith: Ht; 6'3 Wt. 290/345 Runblock 75 Pass block 78, GPA 2.6)
I would train him (60 Sk 40 st). His GPA is fine, his skills will do, but his weight is really low. So I needed to beef him up. And if I am stacked at OL then I won't need him to be out of position. But do not spend too much on strength otherwise you will get an overweight sucky player.
Both size and skill are important for these.
Some RBs, esp. from the ATLE and MW, are big as hell (6'2 250 and whatnot) so the linebackers must be large. I like my linebackers to be 6'1 or taller and at least 250 lbs. Halfbacks are different. If you want to run up the middle more (which I do) you need big juicy halfbacks.
ex. HB Ho Bo: Ht. 5'11 weight 205/235 running 60 route running 65 hands 59 GPA 3.51
I would train him (70 sk, 30 st). His grades are good. His skill set is average so that can be used to beef him up a little. But his big weakness is lack of size, and so using a bit of strength points to bulk him up is good. But not too many, you don't want him fat.
So that's training. Any questions, ask away.