If you have the installation instruction - check the required size of wire needed and compare with what has been installed. It seems that when additional current is needed for heavy load operation, the voltage drop due to undersized wire causes the device to think the battery is low. You can also check this condition by running the engine when it raises low battery alarm and see if the trouble goes away. Using a digital multi-meter measure the voltage across the -ve and +ive near the motor and see what it displays. You may have corroded connection along the wires.
 

Does it have a setting for adjusting the alarm threshold?  My unit (different model) used to give me an alarm and I adjusted the setting lower by about 0.5V so that it would only alarm if the battery was truly low...

For anyone considering a wheel pilot, these are too small for this boat.  The below deck models with a tiller arm to the rudder post have the strength needed for a boat our size.  Following and quartering waves will eat that little wheel pilot alive.  Then you're the autopilot!  

I have to agree with Knot Done Yet that a wheel pilot would be too undersized for our near-20,000 pound boat. For further background information BEFORE you make a purchasing decision I suggest you read my article describing my installation of a Raymarine below-deck autopilot on my boat; article available in the C-36IA Technical-Upgrades library . 

Although the under deck option is far superior, Phil has already purchased the wheel pilot as I did (was on a budget).  I too had the same problem and ended up increasing wire size (not at boat and can't remember exact size) which remedied the low battery problem.  It is also important to have a separate power source from the network power.

With the wheel pilot you will just need to know the limitations.  I do plenty of offshore sailing including delivery from Annapolis to Newport every year outside.  I have identified certain angles, sail setups, and wind strengths that are more prone to Autopilot failure (not able to hold course).  On the whole, the EV100 wheel pilot has out performed my expectations but it does have it's limitations.

That said, I have just purchased a rudder angle indicator which I hope will narrow the bands that the pilot can not keep a course.  The literature states it is not needed but I have heard from multiple sources that it makes a big difference.  If anyone has before and after rudder indicator results, I would love to hear them.

Yes, I read that he already had purchased the wheel pilot; however, I wanted to make my comment about a below-deck autopilot easy to find by anyone doing a search on these forums at a later date. Didn't mean to be critical, only to alert future A/P installers.

Adequate wire size is an important concern on an autopilot servo installation. [Actually it's important on all device instalIations, most especially on high load systems such as autopilot, windlass, radar, HF radio, etc...the typical high load users on a boat like ours.] Wire size is important for two reasons: 1) so that sufficient power needed by the A/P makes it all the way to the A/P servo, and 2) to validate that the correct circuit breaker amperage was selected for the wire size. 

At the risk of being redundant, let me restate that. Circuit breaker sizes are selected in relation to the gauge of the wire that is connected to them. Here's the logic train: A) Choose a wire gauge that gets the power to where you need it to be, in this case to the autopilot computer, and thence to the autopilot servo. Heavy wiring = more power at the using device, because there is less loss in the wiring. B) Then choose a circuit breaker to protect whatever wire(s) is downstream of the circuit breaker. The purpose of a circuit breaker is NOT to protect the autopilot; the purpose of a circuit breaker is to keep your boat from catching fire if the SMALLEST wire downstream of a circuit breaker shorts to ground. 

So as you rewire your A/P, please make sure that the circuit breaker size is appropriate for the wire size you have installed. When you install your A/P circuit breaker, make sure that the prior owner or someone else in the past has not sneakily attached some small wire, like an 18 or 20 gauge wire, to tap voltage 'conveniently' off to some radio, or spotlight, or who knows what other equipment that might be hidden away. If you put in, say, a 20 Amp circuit breaker to protect your new A/P wires, and that hidden tiny wire shorts, that small gauge wire WILL glow red hot, and probably set your boat on fire. 

A friend told me to be able to update thr Raymarine autopilot you need to do it thru a Raymarine chart plotter, I have a Garmine 4208, is there another way to up date the autopilot?

On Island Girl I have a 50 amp Sub fuse panel installed on the Aft Bulkhead next to the Auto-pilot computer. All the Pedestal electronics are powered off this panel. It's feed with a # 6 wire .Very short wire runs from there to Pedestal Radar, Chart plotter, Auto Pilot and wind.

Although I would have preferred the EV-200 below deck Pilot the EV-100 has been working well.
The EV-100 uses the same drive as the ST4000 unit which came on a ton of C-36's. The EV-100 just has a ton of improvements in the way it responds. IMHO.
There has been a couple of software upgrades in the last couple of years. I would call Raymarine to answer your Garman question.