Just went on a shopping spree to acquire and try each and every available ship. Enginnering them is part of the testing, so lots of hassle swapping things around.
Some findings: there's option to store multiple modules, but didn't see an option to fit multiplr.
So, my storage methods:
* I use the 20 of 60 module slots as swap slots to store multiple and manually install modules.
* Ships are located around the bubble where my activities are. Example: I have a multi-purpose Python and an Eagle around Maia. Eagle is actually for engineering small thrusters that my EngineerConda can't fit.
* I specify roles for S/M/L ships: L miner, M miner. S combat, L combat, etc.
* I use similar ships in the size/role combo as storage and swaps: viper 3 with rails v viper 4 with Beams, etc.
* Remaining 40 of 60 storage slots are used for extras like c4 hardpoints I don't have enough ship slots to fit them in.
I could see myself using the extra 60 slots in 3.0 to store c4 hardpoints given the G1-G5 process for each new type of engineer module.