Hello, first time with Divine Divinity, I guess it will be more enjoyable the first time through.

1-I read the manual, but could not find the alchemy skill as a mage. There is suppose to be a 'Way of Lore' but I don't have access to it for some reason.

2-Why can't I save both soldiers if I found a healing gem at the fountain, how do I give the gem to the reptile-man or even use it for myself.

3-Is it possible to close doors behind you, seems it would help you steal easier. You can close barrelsetc to conceal your crimes.

4-What happens to any AI helpers if you leave a dungeon, can you get them again, can you equip them?

Any advice appreciated, thanks.

Open the skill window and switch to the survivor skills; Alchemy in in the top right group of skills (way of lore). There is a button on the left between the skill groups which will toggle showing all skills or just available skills. Level 1 of Alchemy requires you to at least be character level 3.

You can not use the healing gem yourself. Explore the rest of Aleroth, and you will find a way to save both soldiers. You need to talk to each patient to use the healing gems, rather than Otho and Goemoe.
Generally speaking in the game, if you see a pile of crates, rocks, etc, check it out, as there may be something behind or under it.

Yes, for the most part you can click on open doors or gates to close them again. This can help with stealing, though NPCs can open doors, as well.

The zombie helper in the Aleroth catacombs will die for good once you leave the dungeon. A summoned or resurrected creature that you have cast Aura of Command on will follow you back to town, etc, but be destroyed if you sleep (eventually you can switch to restoration potions and not bother sleeping).
You can not equip any minions. You can right click on them to cast Restoration, Aura of Guarding and SpellShield, though.

Free skills, and spell books you can buy

wow, you answered all my questions ...thanks alot. I am also aware that you have something to do with Larian, so I must say that this old-school RPG is a godsend for people who can't get into the new 'style' of FPS , oh I mean RPG.

So thankyou on both counts, I am really enjoying the game and can't wait to face the orcs and the dangerous world outside the village.

EDIT(can anyone help me with these last few probs): Seems impossible to close a door behind you, but is possible while standing in front of it. If you do manage to close the door while seemingly behind it, he will open the door as you walk back into the room.

I am still having difficulty with alchemy, the manual and the book in the game say you can put an empty bottle on an herb and it will create a potion, I fail everytime as it says he doesn't have the skill to do that (after unlocking alchemy skill). I can combine potions now though but had hoped to make potions from the red mushrooms and other herbs near the alchemy book in the first town.

If you summon a skeleton it never follows you very far.

On a positive note ... I was finding it very difficult to cut through the relentless hordes after the gateway in the first dungeon. Then I discovered how to teleport and change my special skills. Awesome. I had only been using meteor strike untill this point.

Is there a particular place you are trying to keep the door closed? You can enter the room, drop a teleporter stone, leave, close the door and use the other teleporter stone to get in.

Also, in the case of stealing, there is an exploit which will allow you to easily steal, to the point of removing all challenge and fun. How do i steal stuff from houses

Level 1 of alchemy allows you to mix potions, level 2 create minor potions, level 3 create normal potions, etc (Alchemy Spoiler Thread).

You can get a level of alchemy from an easy quest in the Dark Forest (Free skills, and spell books you can buy).

You need to cast Aura of Command on summoned or resurrected creatures, or scorpions (from the Deadly Gift skill), to get them to follow you (higher levels of that skill allow you to have more followers). You can also cast Aura of Command on creatures opponents summon, to turn them to your side.