I don't think there's any such thing as an ATMega32UC3B. There's an AT32UC3B, but that's a 32-bit UC3, not an 8-bit AVR, let alone an ATMega. If that's what you're talking about then the pinouts will certainly be different--they don't even have the same pin count!
Generally with AVRs the first number at the end indicates the flash memory size--so an ATMega32u4 should be the same as an ATMega16u4 except the former will have twice as much flash (and usually twice as much SRAM and EEPROM) as the latter. Check the datasheets to be sure, though!