I figured it out yay
Ok to make the region show "blue" instead of green as it dose when you shoos every other faction just go to Step 1 and make the field that shows what faction owns the region blank: main\startpos.esf\CAMPAIGN_STARTPOS\CAMPAIGN_PREOPEN_MAP_INFO\REGION_OWNERSHIPS_BY_THEATRE\REGION_OWNERSHIPS_BY_THEATRE\REGION_OWNERSHIPS\REGION_OWNERSHIPS
Step 2, change the last field of the faction you have choosen to take the region from and change it to the right owned regions as for me I made a rebel region of one of Swedens regions and thus decresing the number of regions from 4 to 3: main\startpos.esf\CAMPAIGN_STARTPOS\CAMPAIGN_PREOPEN_MAP_INFO\FACTION_INFOS\FACTION_INFOS
step 3, go into the rebel faction and extract the faction ID to make it more easier I usualy mark the id number and then press ctrl + c And then the id is copied: main\startpos.esf\CAMPAIGN_STARTPOS\CAMPAIGN_ENV\CAMPAIGN_MODEL\WORLD\REBEL_FACTION\FACTION
step 4, go into the regions manager and find the region you have choosen and copy the id into the 16th line where it says "Controlling Faction ID": main\startpos.esf\CAMPAIGN_STARTPOS\CAMPAIGN_ENV\CAMPAIGN_MODEL\WORLD\REGION_MANAGER\REGIONS_ARRAY\REGIONS_ARRAY\REGION
step 5 Save the changes and start the game!
the flag of the region is red for some reson but I haveent had any problems with it so far, the region starts with no rebel forces sins you havent added any yet, it is possible to retake the region as usual
enjoy