You'll be fine. I've go this on my Sv as a phone charger. The voltage variation is around 2 volts in 12. This equated to around 0.8 of a volt in the 5 that is phone is using. I'd use a 1-2 amp fuse as the currents will be minimal.
Based on the Sv,
I'd connect both to the battery. You then have a large smoothing capacitance to remove any junk the alternator throws out. I'd use 20AWG, preferably tri-rated, with a proper automotive blade fuse and an inline switch to turn it off.
Make sure you double cover all exposed contacts to a protect from fretting to the frame and to waterproof. As Dave says make up a little loom as you go, (it is easy trust me) to keep it tidy and consider where the cable will sit to prevent trapping, flapping and fretting.
