When you earn EXP, you will be able to allocate it to a specific job to fill up the exp gauge. For example, if you earn 100 EXP for the month, you can choose to use it all for your active job to learn the 50 EXP skill and the 100 EXP skill, or split it between Active and Passive to learn the 50 EXP skill for each job. When you have spent a total of 1000 EXP on a job, you will have mastered it (except for Freelancer and Warlock).

So it will work more like the second way you mentioned, filling an EXP gauge for each job asterisk you take.

(Also, when you learn your 500 EXP skill for a job, you will also unlock the job's modifier skill as well.)