I haven't used VXA, but I can't imagine the eventing is much different from VX and XP, so I'll give it a shot.
Each skill would need 2 unique variables: one for the skill's XP and one for the skill's level. If you're doing, say, a fishing skill, then simply make the act of catching a fish (and attempting to catch one if that's how you want it) increase the "fishing XP" variable by a certain amount. Then, in the same event, have the game check what the "fishing skill" level is, and based on that number, have it check if the "fishing XP" variable is greater than or equal to the amount needed to level up. If it is, increase the "fishing level" variable by 1 and set the "fishing EXP" variable to 0.
Alternatively, you could simply never reset the XP variable and have it simply set the skill's level based on the amount of XP.