Hi MAB
I would spread your compost / manure on your patch now, then cover it as Rustylady suggests. This will help to not only suppress the weeds but assist in the compost being taken in by the worms and other beasties without loss of too many nutrients by leeching over the winter months.
Lift the covering in sping, and it should be easier to dig out any weeds that are about.
Alternatively you could spray with a glyphosate weedkiller (Roundup for example) and thereby create a stale seedbed to sow and plant in.
Other than not removing perrenial weeds you did right to just dig them in - all plants pull nutrients to the surface to some degree and you have just put all that goodness back into the soil.
As for organic - organic growing is an ideal - I try but I use weedkiller on bare ground - and you cannot see any of my crops for weeds at the moment. So don't get into a pickle about it - just do what you think is right for you. At the end of the day, you need to enjoy looking after your patch - the moment it becomes a chore, is the moment you lose interest.
Good luck and above all, enjoy.

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Rat

British by birth
Scottish by the Grace of God

Blog updated Wednesday November 13th