Follow the instructions in your literature procedure.
For an aqueous workup of most organic compounds this will involve:
Diluting the reaction mixture with a solvent for workup
(this is the organic layer). Exceptions
Washing the Organic Layer with various aqueous solutions.
Some of the byproducts generated during the reaction will be neutralized
or removed by dissolving in the aqueous layer.
Examples.
Ideally, the two layers will be clearly visible.
If the result is one cloudy layer, you have an emulsion.
Drying the Organic Layer with one of the drying agents.
Filtering off the drying agent.
Rotoevaporation to remove the solvent.
The residue left is the crude product, ready for diagnosis.
Certain types of compounds are more difficult to isolate than
others--if your product might be volatile, soluble in water,
charged at low or high pH (e.g. an amine or a carboxylic acid),
unstable, or possesses stench, see
How to Handle.
Put a flask under your separatory funnel before pouring anything into it.
Aim for a homogeneous solution: keep adding either solvent or an aqueous
solution until all solids are dissolved. If solids are insoluble, see
troubleshooting.
When washing with aqueous bicarbonate, vent the separatory funnel
often to prevent pressure buildup from evolving carbon dioxide.
Pay attention to what the layers look like. If the aqueous layer
looks swirly, or both layers are colored, you may still be removing
aqueous soluble byproducts. Try another aqueous wash.
If you think your compound may be soluble in water, TLC the aqueous layer.
Always wash the organic layer with brine last.
Keep the aqueous layer of an extraction until you have an NMR of your product.
After rotoevaporation, store intermediates neat in the refrigerator
or freezer.