Unfortunatley I can't suggest a good way. The effort in MT goes into keeping the content separate. So its the equivalent of asking to combine two different repos.
It then becomes a data migration exercise that will be dependent upon your data and requirements.
It could be fairly trivial or it could be fairly hard.
For example you may or may not need to map your users and with it their access control.
Or do you have overlapping/conflicting content such as file names, models or categories? How do you resolve those conflicts.
There will be various tools that can help, but it will need to start with some analysis of your data.