Is there a way to automatically assign each territory to its corresponding bonus, or do I have do check each one manually?
And any other tips on making a diplomacy? Thanks.

Each territory has to be assigned to its bonus manually. This can be time consuming but if you want to do a diplo map, it has to be done. Also depends how big the map is?

A few tips:
1.Draw the map outline (and territory seperation) with smooth lines, so the whole think doesn't look messy. Then draw the whole map before anything else including territories.

2.Now that you have the territories create your bonus shape. Duplicate this shape into every territory to see if it fits. If not you may have to make adjustments.

3.Finally upload your map on to warlight. Fill in all the territory names first. Then copy-paste all the names of territory's into the bonus distribution, then assign to each territory.(Even though you haven't done the bonuses yet)

4.Last part-tiring part-fill in all bonuses on the map on inskape. However then upload again onto warlight, the whole map will have it's bonuses already assigned to each individual territory. This mentally helps for me.

it depends on what it is, is it a real-time map or a fantasy one?

And no , It happens all manualy. Making a diplo map is harder than you thought.
Also giving person preference in numbers of Bonusses can make other people hate you.