There are several ways you could do this.
One is to keep a Physical Fitness journal for each child. This would be nice if you want to include photos.
Another way is to create P.E. courses and add benchmarks that are appropriate to the age/grade, such as "Complete 1 pull-up," "Flexed arm hang for 20 sec," etc.
Then, as your kids reach these various benchmarks, you could record the dates to mark progress. Benchmarks are printed out using the "Progress Report," which could also include any written assessments that you may want to record for each child.