I think the following should answer most if not all of your questions.
1. Create a new SDC file named <something>.sdc
2. Add the following two lines to the SDC file:
derive_clocks -period 10.000
derive_pll_clocks
These two lines will derive all base clocks and give them a 100Mhz constrain. It will also derive all PLL clocks in your design.
3. Add this SDC file to your project.
4. Open TimeQuest and run "Update Timing Netlist"
5. Now at the command prompt type "write_sdc -expand <something>.sdc
6. Now you can open <something>.sdc and change the generated clock names and change the frequency of all the base clocks.
Note your new SDC file now has to be manually changed every time you change a setting in the PLL MegaWizard files that effects timing.
Have fun.