I generally use anything between 1000 mA and 1800 mA. The only reason to use a rate lower than 1000 mA on an AA cell is if it has a high internal resistance due to age and wear. This is not likely to be the case with an eneloop that sees regular use.
To find out whether the batteries are being overstressed by your charge rate of choice, simply feel them at the end of charging just before Done appears. If they are cool to the touch there is no problem.