I made my own tool to remove the smaller bearings, start watching the video around 5:00. You could accomplish this various ways, using sockets, etc. I saw that Santa Cruz is now including a spacer between the bearings, and you're right, this bearing removal tool won't work if there's a spacer. The spacers I saw had a notch cut in the end so you could stick a punch in from the opposite side and hit the edge of the bearing (since the punch would fit through the notch). You would then work your way around the bearing until it is fully removed. Once the first bearing and spacer is removed, you could use this tool to remove the second bearing, although you would probably just use the punch again.

The tool for the larger bearings I purchased directly from Santa Cruz, just search their website and you should find it. They also make a smaller version of it, to fit the smaller bearings in the upper link, but that one didn't work that well for me so I made my own tool for the small bearings. I think you can purchase similar style tools from companies like RWC.