There is no "best way" to set up LMCE, it all depends on your needs/wants, the possibilities in your area (mainly reception issues) and how much time and effort you are willing to put into building your own personal custom system.
You'll probably want to start by looking at the options available for receiving a TV signal. For 2 TVs you will need either a hybrid and one media director, or a core and 2 media directors. For watching different channels on them, you are likely to need at least 2 tuners, maybe more if you want to record shows simultaneous as well. Unless your TV signal is DVB, then it is sometimes possible to watch/record more then one channel per tuner.
To get started you can find the experience of other people with their hardware in the wiki:
http://wiki.linuxmce.org/index.php/Category:Hardware
