The skills are there for you, you just need to get them on your taskbar...
Hit "P" (I believe that is the shortcut) to bring up all your powers and you will see them all there - drag the ones you do not see on your taskbar. That's it.
Also, so you know, the skill points you add when you gain these points (the ones that for Lt. cost 100 each) --- all they do is make the corresponding skills they represent better. For example, as an engineer, if you spend 100 points to make Eng. Modifications better, you are making specific ground abilities, such as mines, better overall - it's how your basic abilities get better as you level.
Sorry had a double post there. Ok so I opened the screen where I add skills to my hotkeys, and I still don't have the abilities mentioned as engineer... I'm basically missing like 2-3 skills! Could it be because I don't have any skill points in most of my enginnering skills? Most of my points are in the skills for phaser and torpedo power and ship management stuff.