You can do that. I did exactly the same thing.
The PIII 600E has a 6x internal clock multilier, and it expects to see 100MHz FSB. I do not, however, know if your BIOS version will automatically detect and set for these default settings. Not too worry though. You can disable the jumperfree mode at the JEN jumper (JEN stands for jumperfree enable, I suppose). The default setting is jumperfree enabled, for automatic CPU detection, etc.) I am not at home (where my manual is) but I used the dipswitch panel to set the FSB. It is well described in the manual. There are settings for 33MHzPCI/100MHzFSB, as well as a few other choices (you should probably start at 33PCI/100FSB, to test it at nominal speed) I actually set it for a tiny overclocked setting of 103MHz, so it actually posts as a 617MHz coppermine. I'd go higher, but this is our business computer at home. We choose stability over performance on this computer.. though it IS really responsive and quick even at the nominal settings of 600MHz. I couldn't resist a slight boost.
Is your 600E a flip chip or Slot 1 CPU ?