The Toyota Belta and the '05+ Toyota Vitz come with the same 1.0L (1000cc) engine, it's known as the 1KR-FE it's a In-line (Straight) 3-Cylinder. The other engine's that the Toyota Belta and Toyota Vitz offer is the 1.3L (1300cc) 2NZ-FE and 1.3L (1300cc) 2SZ-FE.
As far as valves are considered each Cylinder has four Valve's. So, the 1KR-FE has 12 Valve's and the other two (the 2NZ-FE & the 2SZ-FE have 16 Valve's).
Now it comes down to which vehicle you want to buy, the Belta and the Vitz are both very economical and enviromental friendly vehicle's. If you have a big family and you need trunk space I'd suggest you to go for the Belta. If space is not an issue I'd say you go for a Vitz. Fuel economy of both car's is almost the same, the fuel economy of a vehicle also depend's on proper maintance.
The rest is upto, which vehicle's shape you like better, which vehicle's color's are better to offer, which vehicle has more additional feature's etc.