Cyclone III Starter Board clock input

This starter board is having a Cyclone III EP3C25F324 device with a 50MHz oscillator supplying the clock signal. For my project we would like to use an oscillator with a higher frequency stability. After searching on web, we found only 100MHz with the desired stability is available. My question is, can I use the 100MHz oscillator to replace the existing one, and inside my project, I simply generate 50MHz clock based on the 100MHz source? After I change the oscillator, will I still be able to program the FPGA through Quartus (or will that affect the JTAG programming)? Thanks.