Works like this:
Go to "Your ability", look for Standing: xxx Next Rank: xxx
When you get the new faction rank, you get X ability points, depending on the difference between previous rank and current rank.
So if you are 0 standing, and get a new rank at 1000 standing, you will receive 1 ability points.
On next rank, you will need 3000 standing, so you will get (3000 - 1000)/1000 = 2 ability points, to a total of 3 ability points so far.
As you progress in rank, it gets tougher to achieve the next rank, and if you change faction before achievement of next rank you will reset the current faction standing, but won't lose the ability points and skills you already have, but may lose some progress to next rank.
When you change faction, the skill % you learned from that faction stays with you and is active,
but you won't be able to increase the skill until you rejoin that faction.For example, if you have 2000 / 3000 standing, and change faction, you will lose that standing and have to start from newbie rank again when you come back. But, you won't lose the 1 ability point you got at 1000 standing.
If you have negative standing to a faction and wish to join them, you will have to work your standing up until it's positive. You won't gain ranks and abilities until you work your standing to a positive level. Think of it as community work

Also, for skills, the more you increase a skill, the more ability points it will require. Skills have importance levels, and some may be harder to increase then others. There is also a max % you can have, usually 50% for "General" skills and 75% for "Faction" skills.