Please include the Lammps user list on all questions regarding Lammps. There are two fixes in Lammps that can do two-temperature models, ttm and atc. I'm one of the authors of atc. If you decide to use the ttm fix, please specify so those experts can help. Your question below is too vague. I suggest starting with the most relevant example problem and modifying it to handle your problem of interest. If you have specific issues with that process, it is more likely help can be provided.
Jeremy