Right - the remote that ships with non-DirecTV TiVos (and non-DVD TiVos) can control two TiVos with the flip of the switch - even DirecTV ones. So you got the right remote. The key is understanding it and programming it.

TiVo was smart enough to realize that people want to do what you're doing: have two DVRs in the same room. So they allowed each TiVo to have a specialized address code, numbers 1 through 9. All TiVos ship set to 0, which is a universal code. Remotes are the same way. Any TiVo set to 0 hears all remotes, and any remote set to 0 talks to all TiVos.

So you need to set each TiVo to a different number (1 and 2 make sense). Then you need to set each 'side' of the remote (each position of the 1-2 switch) to work with the appropriate code.

TiVo has instructions for pulling this off (it's not too hard) on their website here. The key is making sure that you are only talking to one TiVo when you do the addressing. You might just unplug one, set the other, then unplug that one, and set the first.