Depends ... if you have a separate EIN for each business then you should enter them separately however if they are all unincorporated single member LLCs then you can also put them all on one Sch C if they are all in the same "line of work or business".
As for the quickbooks the same rule applies. If they all have separate bank accounts you could choose to keep the books separately however there is no rule that they cannot be combined. Either method will work ... it is more of a what is better for your recordkeeping or situation.
