So first as everything is based on Bonus points let's talk about them, how many our main character has and how can he increase them.
So initially our MC has 99 bonus points.
But he has added 1 point to a very essential skill 'Character Reset'. So think of it like 1 point which he can never remove as that skill is the thing which allows him to use the bonus points freely.
Another skill which is an essential skill is 'Appraisal', which is like an 'identify' skill. It also costs 1 point.
So you can take it as that at the start of the story our MC has 97 Bonus points which he can use.
Now there is only one way to increase the bonus points and that is to increase the level for the first job/class you have.
The BP calculation goes like Total amount of BP = 99 BP + (The level of the first class -1 )
Or for the story removing the bonus points for the 2 essential skills it would look like
Amount of BP he can/would use = 97 BP + (The level of the first class -1 )
Spoilers:
I said first class/ job because there is a skill which lets you add extra jobs and change their orders too.
For eg. Suppose the MC has 3 active jobs, Hero Level 2, Thief Level 3, Villager Level 4. In this order. So Hero would be his first job, second job would be thief and third would be villager.
So his total BP would be 99 + ( 2-1) = 100. We used 2 because that is the level of Hero which is his first job. So even though Villager and Thief both have Higher levels than Hero they don't count. If he wants to use their levels then he has to change the order of classes/jobs through a different skill. The same thing is for inactive jobs.
So only the level of the first job matters in BP calculation.
Sometimes our MC won't put the highest level job as his first job. It is because your first job is shown in your ID card and hence you can only put what you can show in the first class or when they are gonna check your ID card change the order of the job so that way you can be safe.