My circuit needs more power than USB can provide (3a) so it will always be connected to an external (regulated) source, but I'm not sure I understand how to keep the USB power separated from the circuit power, so they can't damage each other etc.
It looks like the MC33269D is the voltage regulator because a regular Arduino can run from 5-12 volts? I don't think I need that because the external power's already regulated to 5v 3a.
External power (via connector) requirement is around 7-12 not 5-12.
It looks like the LM358D and NDT2955 control powering the circuit from USB or external power? If I know I'll never power the circuit from USB can I just leave all that out?
Yes, you don't need to copy the auto-voltage switching circuit.
Is the fuse F1 just to keep the Duemilanove from drawing too much power from the USB host? I don't see one in the schematic for the Nano and since I won't be using host power can I leave it out?
Yes, the fuse is to protect from pulling too much current (>500ma) from the host PC. As you are supplying
power via a external voltage source you don't need to protect the PC USB power supply.
Finally is there anything else I need to do to protect the host from the circuit, and vise-versa?
No, as long as you aren't drawing current from the USB cable you should not need any extra protection. Note the use of 1k ohm resistors from the FTDI send/rec pins to the AVR rec/send pins, they are a useful isolation method if you need to use pins 0 and 1 for other purposes after you upload your sketch. If you are only going to use pins 0 and 1 for serial communications you don't have to use them.
As always, thanks for your help.
There are some awful cheap USB serial cables avalible on E-bay if you don't want to build the FTDI circuit. You probably can't get a FTDI chip as cheap:
http://www.ebay.com/itm/370532286388?ssPageName=STRK:MEWAX:IT&_trksid=p3984.m1423.l2649
Lefty