There aren't any easy answers to your situation. The right way to go about merging the organizations is really going to depend on exactly what resources each company has in place, and on what the new administrative and user access models are going to look like. If both organizations are going to remain somewhat seperate, then you may want to think about using forest level federation. That would allow you to maintain seperate Active Directory forests, but still grant access to resources in one forest to groups of users in a seperate forest.

There aren't any easy answers to your situation. The right way to go about merging the organizations is really going to depend on exactly what resources each company has in place, and on what the new administrative and user access models are going to look like. If both organizations are going to remain somewhat seperate, then you may want to think about using forest level federation. That would allow you to maintain seperate Active Directory forests, but still grant access to resources in one forest to groups of users in a seperate forest.