It depends on the product you used. Maybe the debris is a result of the way your biocide kills the bugs. You should be able to setup a circulation
pump and run thru the existing primary w/o manual
cleaning.
My
current boat sat 6 years, no conditioner and had little care before that. I used algae-x and later switched to Archoil 6200. And to make a long story short, after a couple years got access to the main tank tops and cut in entry
ports an entered the
tanks. 3 600 gallon
tanks were clean. No
water, no sludge, no build up in the bottom. Whatever was there apparently dissolved and was caught in the filter w/o notice. After the first primary change I ran 2 micron w/o problems. I always add Archoil 6200 every fueling. Filters got changed about 500 hours w/o clogging.
I've been around
marine diesels for 60 years and never had to manually clean a tank. Even ships that were mothballed 20 years. But the
diesel was better then. I always reconditioned the existing
fuel and cleaned the tanks with filters, additives and circulation. If you're running an
engine that pumps and returns large volumes of
fuel, just using the engine should clean the tank. Keep spare filters. Use a good conditioner at fueling.