Yes, make sure you never exceed about 20 pokemons per box. Otherwise, you won't be able to access the mentioned box anymore and if you didn't save beforehand, your game will freeze and you will lose everything since last save.
However, if you share the load on several boxes, you can have as many pokemons as possible (ie about 20x18=360).
If you have already filled too much your first box, just catch a few more until your pokemons are sent to the second. You will be able to access the PC again via box2 but you won't be able to use box1 anymore until future versions of the emulator are released.