AVR-Chat

I am working on adding 2 wheel encoders to my robot. I am thinking of
using either PORTE5, PORTE6 or PORTE7 but I am wondering if this will
conflict with my PWM which I have on PORTE3 and PORTE4 (PWM output A and
B of timer3) 

PORTE5 - External interupt 5 input or output compare and PWM output
compare C for timer counter 3
PORTE6 - External interupt 6 input or timer counter 3 clock input
PORTE7 - External interrupt 7 input or timer counter 3 clock input
capture trigger

If I use these will they cause problems with my PWM?