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First let me say two things 1) THIS GAME IS AMAZING 2) DAMN BRIAN FARGO damn you to HELL!!!
Okay now that's of my chest my question) are the skill increase by putting using skill points or usage (or both)?
I know there are trainers for advance skills but what about your beginning ones?
This question / problem has been solved by Crosmandoimage
Once you have at least 1 rank in a skill, that skill can be raised by repeated use of it, or by spending additional skill points at a library (not usually worth it).

Skills increase faster if you are successful against tougher checks. For example, if you are shooting rats, your pistol skill will rise slowly. If you are shooting high level robots, it will rise faster, but only if you can score a hit.

Some skills are used so infrequently in the game that there is essentially no way to raise their level through use.
I really wouldn't encourage any new players to go putting points into skills like "Metallurgy" or "Cryptology" at party creation even if they sound cool, because those odd utility skills are used maybe once in the whole game.

Of course you can play anyway you like, but my suggestion would be: keep rolling until your characters you create have at least 17 or 18 IQ, in skills give them 1 point in Swim and Climb, 2 or 3 in Pistols, and 1 in Assault Rifles, SMG, or AT-weapons, and 2 in Medic, all your rangers should have Medic so it doesn't matter which one goes down, the other will be able to get him back up.

As for non-combat skills, 1 of your ranger REALLY should have 2 in Lockpick and Perception (the ranger at number 1 slot should have the Perception), if you have space 2 in Bomb Disarm can be useful, it's only used like 3 times but as you probably guess it can help.

Use lockpick on doors, and if you see stuff that looks interesting, a dead body, a table, rubble, pretty much anything that looks interesting and especially if it gives you text info when you walk on it, use Perception on it, good way to find loot.

And hold down ESC in safe areas to heal.