Is there a way for me to command Virgil to cast Heal on Magnus? Thanks

Magnus is... technically inclined, so Virgil usually doesn't even bother to try. You see, there's this magic/tech negation tomfoolery around.

Healing salves, bandages and other techy stuff is your way around Magnus' health problem.

I see. Am I able to direct/select party members skills or choices at level up, like selecting a certain tech skill for Magnus? Or are they preset? Thanks again.

They're preset. There might be a fan-made mod that lets you pick skills for allies when they level up, I'm not sure.

Preset but can be edited. You need the undat utility and the file is in arcanum4.dat for 1074 or Arcanum5.dat if you're using UAP. File you're looking for is gamelevel.mes in the Rules folder. Mes files can be opened in any text editor and it's pretty simple to do. Once you have it edited just make a folder name Rules in Arcanum/Data and put your new gamelevel.mes in there. IIRC you need to start a new game for the changes to take effect.

NPC schemes look like this:
{93}Magnus {Melee 4, Smithy 1, ST 9, Mechanical 1, CN 9, Dodge 4, MaxHPS 50, Melee 8, Smithy 2, ST 10, Mechanical 2, CN 10, Dodge 8, MaxHPS 60, Melee 12, Smithy 3, ST 11, Mechanical 3, CN 11, Dodge 12, MaxHPS 82, Smithy 4, ST 12, Mechanical 4, CN 12, MaxHPS 100, Melee 16, ST 13, CN 13, Dodge 16, MaxHPS 120, Melee 20, ST 14, CN 14, Dodge 20, MaxHPS 130, ST 15, CN 15, MaxHPS 145, ST 16, CN 16, MaxHPS 160, ST 17, CN 17, MaxHPS 175, ST 18, CN 18, MaxHPS 190, ST 19, CN 19, MaxHPS 210, ST 20, CN 20, MaxHPS 400}

NPC's follow the scheme from beginning to end spending points as they level up. Stats are obvious. MaxHPS/MaxFatigue is +4 per CP. Magick and Tech disciplines go 1, 2, 3. Skills have 4 ranks/level so divide by 4. i.e. what you would call Melee 2 shows as Melee 8 in the gamelevel.mes. IIRC the relevant stat will be increased when raising skills. i.e. a NPC with DX 9, Melee 2(8) would raise their DX to 12 before increasing their melee skill.

If you want to change their starting stats the easiest way is to use a savegame editor. I never could identify a proto and using WorldEd seemed like too much of a pain.