Bonuses can be chosen every time you hit five levels, so at levels 5, 10, 15 etc. You get one choice for every five levels.
You must choose one of the first five bonuses in the list before you can choose any of the higher levels.
Each of the first level bonuses have a "set" of 5th level and higher bonuses that it "unlocks" to choose, so unless you have all five of the first level bonuses chosen, you will not get all of the higher levels unlocked, only that set which goes with the first level selection. So I would suggest that before you choose, you look at all of the options by clicking on read more. First level bonuses cannot be changed at this time, so once you pick it, it's yours.
Colors? The colors Nef has posted is for firefox, which is the recommended browser for VHR, so if you don't run firefox, the colors may be different. For IE, the red is correct, but for selected bonuses, the color is bright green and for bonuses available to you, the color is dark green.
Super Studs is focused on studs for those ranches who's main goal is putting studs up for the public and opens up further bonuses in this group.
Money Grubber is for those folks who's main purpose on VHR is to make money and opens further bonuses for those who don't like to give a dollar and want as much as they can.
Better Breeder is for breeding ranches who want the best foals out there and opens up further bonuses to this end.
Tenacious Trainer is for training ranches who only want to turn out the best trained horses and opens up further bonuses in the same family.
You can spend all five points to select the first set of bonuses, or you can choose to specialize and move on to the second set of bonuses that are available after you have selected one of the first set and have at least 5 levels. Likewise, you must pick a bonus from the second set in order to open up or unlock the third set of bonuses that are available after you reach level 10, then again for level 20 etc.
With the exception of the first set of bonuses, you can remove a bonus to select another, however, it will cost. And each time you change your mind, it will cost more.
There is a current cap, but that may be lifted/extended in the future... I know I've forgotten something, but maybe this will help a bit.
Oh yeah, you gain experience and levels through breeding, training and eventing. Nef installed a nice little bar that tells you how far you have to go to the next level.