It depends:
Double sided or single sided board?
If double sided, are the SMD parts topside, bottom side or both?
Which specific flux and what process temperature?
How do you clean the board, and with what solvent?
Is the flux likely to cause contact dermatitis?
In general, I would manually clean up flux as I go on double sided boards with top side components, because its easier with better access before taller components and through hole parts are fitted. However if you are set up with the right board washing equipment and flux, intermediate cleaning is a waste of time, money and effort.