Hi Steve,

The NMEA A and NMEA B wires are completely isolated from the rest of the
circuit. NMEA B is not a ground wire but you do hook it up to the ground of
the GPS.

The ground wire to the autopilot is the same ground as from the computer.
The isolator only isolates the input to the computer.

Here is the complete cable designation info:
Yellow wire-- NMEA "A" (recieve Data)-- connect to GPS output wire
Green wire-- NMEA "B" (signal Ground)-- connect to GPS signal ground wire

This is correct info, although the NMEA "B" is not a ground, it is
'floating', aka isolated from anything, only connected to the circuitry
inside the isolator, just like NMEA "A"

Red wire-- Capn Transmit Data-- connect to Autopilot input wire (and/or
GPS/Radar input)
BlackBrown-- Capn Transmit Signal Ground-- connect to AP input ground
(and/or GPS/Radar ground)

This is also correct.

So far I have ignored the Capn Transmit Signal wire and it isn't hooked to
anything. My GPS is recognized and working fine with the software..
However,
eventually I want the navigation software will need to send XTE to the
autopilot..

I always assumed that XTE would be sent via the NMEA sentence.

I can't figure out what to do with the extra ground wire.

Well you have to connect it to the ground of the autopilot.

This is can all be pretty confusing, it has to do with so called "single
ended" interfaces and "differential" interfaces. I have written a web page
about this, which describes all sorts of connections between these two types
of interfaces. You can find it at
http://www.shipmodul.com/en/connections.html
In your case, the connection from GPS to the isolator compares to figure 4
and the connection from the isolator to the autopilot compares to figure 2.
The isolator only isolates the input (GPS) from the computer, not the output
that goes to the autopilot.

Regards,
Meindert