I started as a humble merchant. I have both ships and I have figured out how to make some good cash. I am wondering if there is a way to fly the scout ship discoverer? I can't seem to get a google hit on this question but I see others saying that they set up the mercury to auto-trade and fly the discoverer ship but I can't figure out how to fly the other ship.
To change ships, you have three options that I know of.
The easiest way is to have both ships docked at the same station. You will then be able to switch ship by selecting the ship you want to get into in the Property section of the menus.
If both ships are in space, close to each other, you can space-walk by pressing Shift and E and move across to the new ship. It's best to give both ships stop orders before doing this, as your space suit isn't particularly quick.
Finally, though probably not relevant at the moment, you can get a transporter device which, when equipped to your current ship will let you transport to another ship within 5 KM.