Not sure which way to go from Rome

I think one reason responses have been slow in coming is that your itinerary poses a common but ultimately tough-to-solve problem: there's no easy way to go between Cinque Terre & Venice, and while your desired locales are certainly beautiful and popular, it's tough to capture them without backtracking...unless you were to fly home from Venice instead of Milan. Here's one attempt to help, though:
-Fly to Rome; visit Rome; train Rome to Venice (through Florence)
-Visit Venice; train to Milan/Lago di Como
-Visit Milan/Lago di Como; train to Cinque Terre
-Visit Cinque Terre; train BACK to Milan for flight home, OR book a discount 'local' flight from Genoa's airport (near Cinque Terre) to the airport in Milan for your flight home

Another option would be to fly from Venice to Genoa and visit Cinque Terre before Milan, and then train north to Milan, for your stay there and flight home. A car could certainly work, too, but I'd be sure you have really good directions and a plan to dump the car upon arrival...it's more of a pain to have the car in Cinque Terre, and Milan, and Venice.

Good luck!

"We're flying into Rome and need to end in Milan. We want to go to Venice, Cinque Terre and Milan/Lake Como."

You didn't tell us how many weeks you will be in Italy. It would help to know how much time we have to work with.

"...we were thinking of taking a day and drive to see the scenery and stop in Bologna or Tuscany cities for lunch"

"Stop in for lunch" makes it sound so easy, but it's a half-a-day job to get into Bologna or any real cities in Tuscany (like Cortona, Montepulciano, Siena), find parking, and walk to a place to eat. Picture busy bumper-to-bumper traffic, narrow streets, strange road signs you cannot read, and people honking at you if you try to pull to the side to get your bearings.

Ok, if you have that pictured, that's just in the outskirts of town. As you get closer to the old part the town (the part you would want to see) everything above doubles, except for the narrow streets, which get even narrower, and sometimes seem to say "do not enter" in every direction.

I hate to sound discouraging, but I'd recommend you have a few days experience driving in the less-crowded countryside before driving into any Italian city.