Hi, not sure what to do when I used all AP points, I tend to stand silly or cover waiting for new AP. Any suggestions what to do, should I manually aim?

Take some jet, or even better ultra-jet.

Yes ... go out and manually aim until AP points recover enough for a head shot. Jet helps but you'll run out there too especially against a super mutant overlord and his Tr-Beam Laser Rifle or Gatling Laser. Hint ... build a dart gun ASAP ... slows them down so you can back pedal away.

Alright, any tips where to aim? Several on same part or different parts queued? I guess same part will cripple easier.

Dart gun cripples in single shot.

I always aimed for the head. Generally the most damage, and the crippling effect is useful.

With the right perks, you can score a kill pretty near every time except against the real monsters.

For enemies that you plan on kiting, dart gun should be the opening shot - it's extremely accurate, so you can often just squeeze off a shot at mid-range.

For combat, I switch to my best VATS weapon (usually a CAR), take my 3-5 shots, then duck behind cover while I reload. Pop out, spray some love downrange, then pop back into cover for another reload. Pop out, use VATS, rinse-repeat.

Sometimes the best tactic at mid-range is to just put lots of shots downrange (or a grenade or two, a missile, or a nuke). Then save VATS for enemies that have gotten too close and need to go down immediately.