2005 FXDL I let the batt get too low in storage and while trying to jump it the flashers flashed twice. Does that mean i need to add water to the batt?

Your bike is flashing out ECM codes. It will flash out the first digit of the code in flashes .5 seconds apart. It will then pause (lamp off) for 1.2 seconds and flash out the second digit. If this is what your seeing it sounds like it's flashing an ecm code of '11' which for a Delphi fuel system equates to 'battery voltage high'.

If you are jump starting your bike from a car, I'd recommend doing so with the car's motor turned off. This is because the charging system for a car is a lot more powerful that that of a bike and you might actually damage the charging system of the bike (blow out the voltage regulator).