I've never had problems with the eastern cities in my seleucid campaigns.

My starting tactic is usually like this:
- change the capitol to Seleukeia
- adjust taxes (very high where possible, low in the rebellious cities)
- get some extra cash by selling my map to the ptolies
- get some cash by destroying all granaries (population growth is usually much faster than I need/like it and they can easily be rebuild later)
- disband the fleets and some unnecessary units
- move as many units as possible to the western front
- kick the ptolies out of Asia Minor and the phoenician coast as fast as possible, your starting units are enough for this
- focus on building roads and first lvl regional MICs everywhere
- then focus on building mines and - where necessary - public order buildings, so that you can increase taxes everywhere

With this tactic you can become really powerful within the first ten years. I usually expand into Asia Minor and the rebel controlled East and then attack either Egypt or my eastern Allies. Actually the AS is one of the few factions you can play without ever going into the negative.