Heal your prisoners and put them into the prison in the city. They will be auto recruited to join its garrison over time. This can even exceed the city's garrison limit, which is probably a bug, but I won't complain while it's unfixed.

In the short term, you'll probably have to stay close to the city. It should take enemy armies at least a day to attack a city after laying siege to it, and you should get a large message prompt that a city directly under your control is being sieged. It's harder to see if a vassal's city is being sieged though. You'll just see the little note in the logs.

No i dont get a big message in the middle of the screen i suppose i get a little one but my eyes and reading skills arent good enough too read them sadly. That with the dungeons i didnt know will try it ty very much. Does the game gets updated different colours for city and armies for each faction would make it much better for me and a big message if a city gets sieged if its yours and vasalls too?

If you're not getting a big message, then you don't have direct control over that town; the leader of your faction or a vassal does. The colors for new factions are randomly generated.

Will try again maybe a bug, but the cities i captured i got them automatically because i started my faction and didnt have any vasall. What i mean with the colours is that i wished the Ai factions had their unique colour and not the static colour of the region of the cities, it makes it very difficult too understand which city belongs to which faction. Hope you understand my points not 100 percent in english but ty for help.

This depends on your goal in current playthrough. The easiest way to prevent factions from attacking your cities is to use diplomacy or captives system.

1. Use diplomacy to request ceasefire with hostile factions. It will take several days. You can declare war on them again later through diplomacy. Remember that it will also affect your standing with their allies. Ceasefire will improve your reputation, declaration of war will decrease it greatly.

2. Capture enemy heroes and expel them if your faction is strong enough. You can strip their equipment before expelling. It will remove them from your current playthrough, so expel only heroes that you certainly don't want to recruit.

3. Capture enemy heroes and offer them to join your faction without releasing them. After some time most of them will agree. If you don't want to have them in your current party, just send them to towns.

4. Capture enemy heroes and carry them with your party as prisoners if you don't want them to join you at that moment, but also don't want expel them. Remember that releasing enemy heroes is a great way to farm talent points and wisdom crystals, so it's better to have some enemies running around until you complete your build.

The reason to use captives is simple. Factions need heroes to lead their armies to attack you. Fewer active heroes means fewer armies. Defeating any hero leading an army sends him to the corresponding town and starts 3-day cooldown before he will be able to leave the town again. The only hero that can't be captured is faction leader. If you capture all other heroes, that faction will be limited to a single active army that you will be able to defeat easily because after every defeat they will lose all units captured by you (and units that suffered 100% serious injury if you're playing not on easy difficulty), so after several defeats such army will be reduced to a bunch of white and green quality new recruits.