The resetting is cuz the variables are tracked inside the scenes which unfortunately resets many important ones. I realized this towards the later end of development and ported some variables over to global variables but we ran out of time to fix it fully.
If you look in the message portion of the game (by clicking on the white envelope from the map screen) and switch to the help tab, there are guides on how the logic node system, upgrade system, and battle encounters function.
You can click and drag blocks onto the gridspace to construct your own ships. You'll need at least one green core block or you can't save or load the ship. If the core gets destroyed the whole ship explodes. The white bricks are hull fragments and the orange diamonds are shooty turrets.
I can paste in the help tips in the description as well.
P.S. thanks for testing it even in its currently buggy build!