It will always be difficult to occupy an enemy settlement that's already pretty well developed.

Some tips:
1) don't upgrade farming any further
2) don't build estates, and consider tearing down estates that already exist
(estates increase population growth and therefore squalor, they also have a public order penalty)
3) check the building browser wich temple deity is best suit for occupying the settlement: the one with the most public order/happiness bonus and wich doesn't increase population growth. Always wreck the enemy temples if they're not from the same culture as you.
4) use cheap, large units for occupation. Akontistai are perfect for this job.
5) The governors house (and its upgrades) give a large culture penalty (except if they're from the same culture of you, in the case of the Romani that's Epeiros, Koinon Hellenon and Makedon). It might be a good idea to let the town expand so that you can upgrade it, negating the penalty.
6) Make good use of retinues that have a law or happiness bonus.