I believe you are on the right track in regards to MySQL innoDB tables. But you must remember that when measuring the size of a database, there are two components: data length and index length.
MySQL database size.
You also have no control over which databases are loaded into memory. If you want to guarantee a particular DB is loaded, then you must make sure the buffer pool is large enough to hold all of them, with some room to spare just in case.
MySQL status variables can then be used to see how the buffer pool is functioning.
I also highly recommend you use the buffer pool load/save variables so that the buffer pool is saved on shutdown and reloaded on startup of the MySQL server. Those variables are available from version 5.6 and up, I believe.
Also, check this out in regards to sizing your buffer pool.