Definately want to clean it with the blower off. I either do it when the temp is up or turn it off. If you try it while running you will have very large blow torch to contend with. Kind of cool to see but not what I would like to work around.
I clean my ash once a week during the heating season. If you skip cleaning it you will fine that you could run into problems. In fact if I find my temp below 180 or I seems to take longer then normal to recover to 185, the first thing I do is clean the ashes out. Most likely the problem is ashes blocking the reaction chamber.
If you are new to the boiler I would suggest cleaning the tubes every two weeks, the damper door area every day and the wood chamber once a month. The tubes and the by-pass door are both easier to clean more ofetn then to let anything build up.