Augments...
 

is there anyway to allow augmentation of armor?

Sure.

Just make sure you're set up to use LDoN and that you have armor with an augment slot on it.

I've noticed though that most it4ems DON'T actually have augment slots unless they're LDoN gear...

But how would i combine the augments with the armor? do i have to make a case or somthing?

Hrm... That's a good question.

There's "birdbath" at each of the wayfarer's camps that you can click on. All you have to do is open it up, put in the item you want to augment and the augment you're gonna use and hit combine!

Now, as to whether or not EQEMu has these "birdbaths" working or not, I dunno. You'll just have to look.