Want to use two Tn pins of the MEGA2560

Hi, I am wondering a method counting pulse instead of keeping interruption ,I read the data sheet of UNO first and use the T1 pin to count the pulse successfully,but I want using two Tn pins to count two pulse source(encoders) ,but there is only one Tn pin in UNO and 4 in ATmega2560 ,but arduino mega board only layout T0&T5 and a T1 pin of ATmega 82U/16U2 a smaller chip between USB and ATmega2560.

1.Can I use the T1 pin of ATmega 82U/16U2? I never knew this chip before .
2.I can’t use T0 pin to count the pulse ,right? because timer0 control the millis(), delay() etc. unless configure the other timers to control these functions.
3.or is there any method I can do?

Thanks.

t1? Explain please. The 16u2 is the USB-Serial chip and if you use it for anything else you will have to use an FTDI to program the 2560.