I think I've done three partial upgrades, and I installed Karmic somewhere around Alpha 3 or 4. Occasionally it is necessary, as when an old package needs to go to make room for a new one. If there's some updates you really want that are being held back, go ahead and select 'Partial Upgrade'. But before you start installing anything, click 'details' and check which packages are being removed. If there is only one or two, check into what they are - chances are they are being replaced by something else you are installing. If there are more than two be very cautious. If there are thirty of forty packages to be removed including gnome and xorg (I saw this once), then use your brains and cancel out of that upgrade.
There is still a chance of severely breaking your system even if you never run a partial upgrade (as in the boot failures of Alpha 5 era), if you happen to update at the wrong time. But for the most part, if you check what is to be installed and pay special attention to anything that it asks to remove, you should be okay. Well, as okay as can be expected when running a testing version of an OS.