External EEPROM or SD would store anything you write to it -- uploading sketches wouldn't affect that.
Whether it's more efficient for you to go that route....it wouldn't be for me 
Doing a little surgery on an Arduino with a $35 programmer makes more sense to me personally than adding extra hardware and complexity. And the programmer is definitely useful down the line if you plan to work with other devices.
If you are really cost conscious you can use another Arduino board as an ICSP programmer. It just takes a lot of reading, experimenting, and patience For me, the AVR ISP is one of the tools I always have on the bench, next to the FTDI serial cable, a couple of screwdrivers, two DMM's, and a cup warmer.
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The Basic Motor Driver: simple, inexpensive motor driver for 1 stepper motor or 2 DC motors