Yes, that is no problem, you can do both in and out over the serial link, it is bi-directional. See for example in setup() of the following code how we send some commands from the Arduino to JeVois, then we get coordinates data from jevois to Arduino over the same link:
note that you have to think about your boot order to make sure the commands will be received (i.e., allow jevois to fully start before you power up your Arduino).
In addition to sending standard jevois commands, you can create custom commands,. Anything that the jevois engine does not recognize will be passed to a function parseSerial() of your module, See
for an example of parseSerial()