Under ship designer options the only thing I see is a scroller for component rotation degree. That's it. Really. I've looked at every other tab and setting, too, and I just don't see this option.

*EDIT I loaded up Dark Avatar just to check out the options menu, and the option for maintaining old parts is clearly there on the Interface tab. It's a checkbox directly underneath the part rotation box mentioned above. But there is a difference between the DA and ToA Interface tab: in the ToA there is an up/down scrollbar on the right-most column, while there is none in DA. Honestly, I cannot "scroll" down below the rotation box in ToA. Any suggestions?

Templates do not store any systems or weapons. They just contain the ship parts and design. Even if you see them in the pics, they are not contained in the template.

Some others have since reported that at minimum resolution the scrollbar is not appearing in the options, so that one is not accessible. For the time being, if you cannot raise your resolution, you should be able to set it manually in the prefs.ini file located at My Documents\My Games\GC2TwilightArnor.