Lets say your a 5th level Magus and you have 6 points to use, When you add weapon properties to your weapon is it also limited levels(aka. For every four levels beyond 1st, the weapon gains another +1 enhancement bonus, to a maximum of +5 at 17th level.) So you wouldn't be able to put vorpal on your weapon till 17th level because it being a +5 weapon property or does it matter as long as you have the points to spend?
You're 5th level. You spend a point and get a +2 on your weapon for a minute. If you activate the pool again, you can change what you spent the +2 on, but it's still only a +2 worth of weapon enchants. You can't activate it twice for a +4.
At 1st level, a magus can expend 1 point from his arcane pool as a swift action to grant any weapon he is holding a +1 enhancement bonus for 1 minute. For every four levels beyond 1st, the weapon gains another +1 enhancement bonus, to a maximum of +5 at 17th level. These bonuses can be added to the weapon, stacking with existing weapon enhancement to a maximum of +5. Multiple uses of this ability do not stack with themselves.
Thus you couldn't burn your entire arcane pool in three successive rounds at level 1 to have a +3 weapon in a fight, which means not only would you need to be level 17, but the weapon you are adding Vorpal to would also need to be at least a +1 weapon, otherwise you spend 1 point to make it a +1 and only have +4 left over for enhancements. Hardly an issue at level 17 but, for completeness's sake I thought I'd toss it out there.