Novella's Secret
You find the first tomb in the game by default. After completing the "Novella's Secret" mission in Florence, you'll find a room full of treasure and see a cut scene that explains that five other tombs are hidden around the empire.
Il Duomo's Secret
The second tomb -- Il Duomo's -- is probably the easiest to find. Stay in Florence and head to Santa Maria del Fiore. Look for a little crack in the wall and simply walk through. As you walk through the building, waypoints appear on your map. Head for each successive waypoint until you enter a large room with many beams and platforms around the outside. Climb around the outside of the room going higher and higher until you can jump to the hanging cage in the middle. You can climb up to the top of the tomb and get the Seal of Iltani, then exit via a window.
Terre Grossa's Secret
Head to Tuscany to find the third tomb -- Torre Grossa's. Head to the district of the same name and look for an arched hallway beside a beggar. Follow the waypoint markers on your map as you scale and fight your way through. When you see the giant chandelier, jump to it and scale its chain to find the main sarcophagus area. Collect the seal of Wei Yu and exit through the ceiling hatch.
Ravaldino's Secret
The fourth secret tomb lies in the city of Forli and is a bit harder to find. Head for the western side of the waterway and jump in the water. Swim around the tower to the north to find the entrance to the tomb. As with the previous tombs, you need to do a lot of jumping to work your way up through the hallways. About halfway through your journey you'll come to a room full of guards. Then move to the eastern part of this area and jump south. Continue climbing until you are above the stables, then jump across, pull the switch, which is on a timer, and race into the now-open sarcophagus room to get the Seal of Qulan Gal.
Visitazione's Secret
The fifth tomb is in Venice in the Santa Maria Della Visitazione area. Climb onto the building and circle around the tower until you find the small nook where the tower meets the roof. Climb inside and confront the guard, who you chase through a few tunnels to a fight. After the fight, exit the room to the south. Use your advanced wall running technique and run across a series of switches and time-triggered columns. The Seal of Leonius is at the end of the course.
San Marco's Secret
The final tomb is hiding on the roof of the Basilica di San Marco in Venice. It's best to get the seal from this tomb after completing the "If at First You Don't Succeed" mission. Use Leonardo's Flying Machine to propel you to the roof, head to the southwest corner of the roof and drop into the recess with the ladder to access the tomb. Head to the organ marked by a waypoint and climb to the top of its pipes, then jump up and grab the switch. The camera pans to show you the next switches in succession. Turn on the switches before your time runs out to complete the puzzle and unlock the sarcophagus and get the Seal of Amunet.