So I am an Engineer but used most of the good abilities in Universal and Engineer. There is an Armor Piercing ability under soldier. If I pick this ability will it only work if I am a solider? Some soldier abilities specify if it will only work as a soldier.

Yes, if your a soldier you can only use soldier abilities.

Same with every other class not including the universal abilities.

Only works as a soldier.
It's an innate ability.
So you resupply your team's or your ammo, you resupply with AP ammo

Thanks. The game really needs to explain things better.

Well, nothing personal, but there are 4 classes each with their own abilities and a 'Universal' section as well; class specific abilities are class specific.