uhm,haven′t played in a while, so could miss out on the details.
anyway with regional criminal mod you can confess to the crime to guards (found the readme to it).For rp-reasons my character usually do that in regions where it isn′t burdened with a bounty,and approach a guard there.
from the mods readme:
"Now there is a new topic "confess to a crime". With this you will be able to tell the guards about your crimes, so you will be able to pay your bounty and clear your name in any regions".