Here is a simple problem I ran into. When I modify a companion NPC, game crashes when I enter the cell where the NPC is.

A. Modifications in CS
I tried to modify a companion in CS (Oblivion). Basically I used Veronia companion from http://cs.elderscrolls.com/constwiki/index.php/Simple_Companion_Tutorial. I wanted to change the look of Veronia and add one of the nice looking http://www.tesnexus.com/downloads/file.php?id=25524. Let's say I want to change Veronia to ImeprialAb, modify her face and hair.

So I opened CS. I loaded the following mods:
* Oblivion.esm
* companion-veronia.esp (set as Active File)
* Abriael_Human.esp

I found Veronia character, opened her properties by double-clicking on her. Then 'Edit Base'. I then changed:
* Race: from Imperial to ImperialAb
* Hair: from HumanFringes to Babehair02Ab
* Eyes: to Flonne30Ab

Next I went to the 'Face' tab and slightly adjusted her hair color: from 70/50/25 to 40/27/13, so it's darker.
I hit Apply. Hit OK. I see the change in the Preview window of CS.

B. Game crashes
Now when I go to game mode, Oblivion crashes when I enter the cell where Veronia is (IC Merchant District). I have both mods ticked under Data in Oblivion Launcher.

How should I do it properly?

The problem you're running into is caused by trying to use parts of one .ESP in another. .ESP files are completely isolated from one another. Try http://cs.elderscrolls.com/constwiki/index.php/De-Isolation_Tutorial.