This is perhaps a dumb question that I should have asked before installing everything

This is perhaps a dumb question that I should have asked before installing everything but:

The strip I bought has JST connectors on either end for VIN, DATA, and GND, but each end also has an additional VIN and GND wire coming out of it (see pic).

I capped those off and waterproofed them for my outside installation. Should I have used them? Is there a benefit or are they a kind of backup or way to add power when needed?

http://i.ebayimg.com/images/g/ZJMAAOSwm0JYDcC3/s-l1600.jpg

Just a backup or an easy way to add external power as needed. You should be able to see those wires going to the same pad as the JST wires on the strip.

they are, just wondered if I missed out on a better/best practice

Yes, they provide an easy way to feed in power on longer runs.