Please note this only applies to soundcard configurations which use multiple PCI cards which are not internally linked together. For example, Aardvark, M-Audio, and MOTU firewire cards (there could be more). Examples of cards which do NOT require this type of sync are MOTU PCI324 and PCI424 cards, RME Cardbus/Desktop/Digiface/Multiface.
Ahh, that is a good question. Your audio card should have a way to select the ‘master’ card (not just the one with internal sync but to actually select this as a master card). For example, in Aardvark cards you can go to the Aardvark control panel, select card#1, press Advanced, and go to ASIO and DirectX and select the Master Aark Card from the pull-down list. You will need to also select card#2 and do the same (select card#1 as Master).
Other manufacturers may have a button which says ‘Master card’ or so.
Audio applications like Cubase and Nuendo will now set the Master card’s synchronization and leave the others as slaved to the Master card and everything should work smoothly.