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 neatly intermediates in the refrigerator or freezer.