Q:

Counting dough...pick up doughs

You have flakes or small pieces of different colors of dough. Do you pluralize these and say, "pick up all these or doughs? 

A:

Dough is considered uncountable like sugar, water, advice and money.
If you need to make it countable you need to introduce a unit. This may be a precise unit like teaspoons of sugar or buckets of water or abstract terms like some advice or all money.
So in yor example, you can either say:

pick up all / all the dough

or

pick up all pieces/crumbs/flakes of dough

