How do I wire two barrel jacks together in parallel?
I want to have two barrel jacks for DC input to my circuit, wired in
parallel, but want clarification on my circuit design. The idea is
that the amps will increase, to power an ATMEGA64, as well as motors,
sensors, etc. more effectively.

Seperate the two power circuits; use one for the motors and the other for the MCU and sensors. Keep the noisy heavy current stuff on one supply and the micro and sensors on the other. You can't rely on paralleling power supplies because usually one supplies most of the load with the other only stepping in to support the other when it begins to sag and that isn't something you really want to happen.
They should, of course, both share the same 0 volts.