I did an engine replacement in April and did the TB/WP with the engine on a stand. Very nice!
When it comes to aligning things up, align the R and L up with the top notches on each side, and crank to the dots(or pulley with 0, if you haven't removed the pulley). It is infinitely easier to align these marks BEFORE you remove the old belt. Remove the pulley and ensure the crank gear dot is lined up with the mark on the oil pump housing. Push a wire into the small hole in the hydraulic tensioner, loosen bolts on the pulleys and remove. Clean and replace WP. Place new TB, the belt may also have markings on it for cams and crank. Just ensure all of those are aligned (and of course, the gear marks) and you'll be ok. Remove wire to retension. Use standard re-tensioning procedure and re-check alignment.
This link has some pics:
Toyota Maintenance: 3.4L V6 Timing Belt Replacement
Woops, I noticed you've removed the belt, in the pics. OK, you have to find TDC on #1 cyl. One way to get to TDC(Compression) on #1 is to Remove the #1 spark plug and rotate the crank clockwise until you feel air rush out of the cylinder and hit your fingers (if you have a compression gauge with a hose, you could use this)...you should be on or near the mark on the crank gear aligned with the oil pump housing. This is the end of the TDC(Compression) stroke and start of the power stroke. If you don't feel air go past your fingers, you're on the exhaust stroke. You'll have to rotate the crank one full turn to get to the compression stroke. Then align the cam marks and you're ready for the TB placement. Cyl 1 is front cyl closest to rad, on passenger side.