^read, watch and learn :)
For the bonussquares:
1. Make a box 15x15 or 16x16 in Inkscape (in the same file as your map of course)
2. Name it: BonusLink_Example (use the name of the bonus where example is now.)
3. save the file.
4. Go to de WL map designer.
5. Go to your map
6. upload the file
7. press "bonuses window"
8. Press "create new bonus"
9. Fill in the name of your bonus (without "BonusLink_" , so in this case you would have to fill in Example.)
10. Change colour and value
11. press "confirm"
12. Press "select territories" (upper left corner)
13. Select a territory
14. Lower left corner you have the option to name your territory and put it in bonus(es)
15. click the bonus(es) you want the territory in and you are done.
I hope that is clear.
You have to make a box for every bonus you make and if you want to make superbonuses like "Roman empire bonus" you also just make a box (or make it a bit bigger, so it is clear that it is a super bonus) and just press territories and put them in this big bonus.
TIP: If you make a superbonus, which contains multiple smaller bonuses, you can just select the smaller bonus and put it in the big bonus at once, without having to click every territory. (just click the bonussquare and lower left corner put it into the superbonus.