Carl,
Place it wherever it produces the best sound. You can do this strictly by ear and get fine results. If you want to supplement placement with measurements, by all means do so. But there is no "best" spot; "best" (or, more appropriately, "good") placement is room / system / individual preference dependent. There are some resources you can look into, including the work of Todd Welti and/or Floyd Toole at JBL, who have studied, and written AES papers on, multiple sub placement.
To answer your other questions, aiming shouldn't make too much of a difference, particularly if it's a down-firing sub. A front-firing sub should generally fire into the room, but, again, specific aiming shouldn't make too much of an audible difference.
The second sub will affect the sound of the other sub in the sense that wave reinforcement / cancellation will occur at some frequencies. Which frequencies and how much reinforcement / cancellation is highly dependent on the location of the subs, the room geometry, and so forth. In general, if you can select initial location(s) where the audible effects of reinforcement / cancellation are minimal, then you've found a good starting point(s).
Finally, I have found that it is sometimes helpful to locate a second sub at a different height relative to the first sub. Whether this is doable depends on your setup, of course. But I have found that this lends more flexibility to achieving the best possible sound with multiple subs.
