The ship designer is an extremely limited tool. You cannot change the Hull size of designs you've made, when you save custom modules they are all mashed up into a non functional clump and not anywhere near the original configuration... If I cannot save orientations, alignments etc. then why bother creating custom mods? I can just use the standard ones and make it again in a few seconds, or save time because I have to set the various variables over again because they don't save.
I don't like the standard ship designs, and with the limited nature of the designer I'll check back in with this game after a few patches. It's not living up to expectations.