Need to write timing constraints for PLL generated clocks?

create_clock -period 40.00 -name {CLK_25MHz} [get_ports {CLK_25MHz}]

derive_pll_clocks

That is most likely it. If you want to cut timing between any clocks, let's say the 50MHz and 100MHz are related but the 25MHz is not, then find the names of the three generated clocks(just run Report Clocks in TimeQuest), and add the following:

set_clock_groups -asynchronous -group {pll_50mhz_name pll_100mhz_name}

-group {pll_25mhz_name}

Most likely all three clocks are related, but just showing it as an example. If just starting .sdc constraints, the following might be of interest:

http://www.alterawiki.com/wiki/timequest_user_guide