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And then I wire the positive lead to Vbat and the negative one to Ground & the ATMega's ground?
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"Also, if I use a battery, do I wire it to the Vbat and ground (and ground to the Arduino's ground) while not wiring Vcc to anything? That's what I seem to understand from the spec sheet. "
Yes. Battery+ to Vbat, Battery - to DS1307 Gnd/Arduino GND.
VCC gets connected to Arduino VCC.
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You will need a coin battery holder:
If there is no need to replace the battery, you can use the batteries
with the leads attached to them (see futurlec "batteries" link above for an example).

--- bill
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