I'm not sure how much this will help but I think you're actually making things more difficult in your own mind. Remember that playing bass is all about the pattern (progression).
As far as a typical bass player is concerened, playing a song in Eb is the same as playing it in Ab. The only difference is which fret you start on (the root).
When people tell you to use scales (major, minor, etc) it's not meant that you should go through an entire song playing major scale after major scale from root to octave. What they mean us to use your knowlege of the scale to add more flavor (extra notes) to the progression. Let's say a song progression is a 1, 4, 5 in Eb. This means that your root note (the 1) is an Eb, the 4 is Ab, and 5 is Bb. Thus the progression is Eb--Ab--Bb.
Since playing the same 3 notes over and over would get boring (to play and listen to) I could add a personal touch to the progression by drawing from my knowledge of the major scale and play something like Eb--Ab--Db--Eb (octave)--Bb. Notice that the two extra notes that I added (Db and the higher Eb) would also "fit" into the music since they are a part of the major scale.
Here's where things could get a little awkward since I personally look at this in 2 different ways.
1) You could look at the Db and octave Eb as being the flat 7th and 8th respectively for the Eb major scale
or
2) You could see Db and octave Eb as the 4th and 5th respectively for the Ab major scale.
That's just something to get your mind moving in the right direction and hopefully I didn't confuse you. Basically here's what I did. I played the same Eb root note, then when I went to the second note of my progression, Ab. Next I played an Db and Eb as "filler" notes before playing the last note of my progression (Bb).
Let me know if this helped. If it is still confusing, feel free to ask and I'll try explaing again or maybe others could chime in with their thoughts!
God Bless,
-J