When you're skinny and want to get bigger, the first step is just getting stronger. At first you really only need to track how much weight you lift each time, and how much you eat (calories).
If you're eating enough, and resting one day between lifting sessions, you should see your lifting numbers go up, every time, for a month or two.
After you've gotten stronger and gained some weight (some of which will be body fat), then you can turn your attention to things like body fat percentage.
I should add, you need to choose the right lifts if you want to be able to see continuous, incremental progress. Big lifts that use lots of muscles (squats, deadlifts, bench, overhead press) will give you that. You can't expect your bicep to be able to lift 5 more lbs every time you hit the gym, but you can expect large groups of muscles to work together to be able to lift 5 more lbs each time.