It is not a problem to use 2 databases from within one script, just do two sets of connections and when you do the query specify what database the query should go to.
But it is hard (not impossible I think) to be able to use the databases together, like linking tables between the databases. I have seen a solution on these forums, but can't remember anything about it.
To be able to answer your question better we need to know exactly how you will use the databases together. Also think about the possibility to expand whatever it is that you are doing in the future to allow not only 2 databases but 10 of them. Normally I would not recommend this, but since you are already talking about 2 databases that should work together you might want to design it to allow you to add databases in the future. It is not much extra work, but you will regret not having done it if you need more databases.
