Just finished the same job in my 94 Rodeo 3.2. The Haynes manual, while thin on some important content generally, had a good diagram and fairly decent explanation of lining up the timing marks. It's easier to understand once you have the timing belt covers off.
Do yourself a favor and get some white out or a silver metallic marker pen and a ruler. There is a recessed line in the metal and a painted white mark on the OUTSIDE edge of each camshaft sprocket, and a dot on the INSIDE (back) of the timing cover (against the valve covers). Problem is, this means they're about 2" apart (front to back) and you'll be looking at it from slightly above since the radiator is in the way of your line of sight to look at it level. Eyeballing this is almost impossible to do accurately. So, touch the silver marker to the dot on the covers to highlight it, and draw a perfectly level line on the old belt (the old line is long gone by now.) This will make it easier to line up.
You need to make sure ALL THREE gears are in proper alignment -the crankshaft and the two camshafts. As a ballpark, this means (on my 3.2 anyway) that the passenger's side camshaft mark will be in about the 10 o'clock position, the driver's side in the 2 o'clock, and the crankshaft in about the 9 o'clock. The mark on the crankshaft sprocket is hard to see, but it should be 180 degrees away from the "keyway" tab on the crank, meaning the crank keyway tab will be at about the 3 o'clock.
God forbid anyone should try to time it using those clock positions only, but they're useful as a general guide.
Once you have the shroud, fan, fan mount, and timing covers off, it will make more sense. To line up the marks, take the drivebelts off and remove the crankshaft drivebelt pulley (you may need a large gear puller), then reinstall the bolt that held the pulley on. Use a 24 mm socket to turn the crank a couple of full revolutions of the belt until everything lines up. When you'd be willing to bet your engine that it's all lined up, you can remove the timing belt and start with the new installation - but remember, this is "one-tooth" tolerance. You can't be even a little off. This is easier said than done, as it's easy to get slack in the wrong place and pull one of the camshafts out of alignment while trying to get the new belt on. If your timing is good now, the goal is to take the timing belt off and DO NOT MOVE the crank or either camshaft until the new one is on and the slack is pretty equal all the way around (in other words, make sure that you have absolutely minimal slack between the two camshaft sprockets where the belt dips down to the water pump pulley - if this is loose, you'll play hell trying to get enough slack to make everything else fit.)
You may have to experiment with different orders of slipping the belt onto the various sprockets and pulleys - I could NOT get mine to go on in the order that the Haynes manual said (crankshaft first, then passenger's side camshaft, then driver's side camshaft anf finish by pulling down onto the water pump pulley) and when I tried, it threatened to pull the camshaft pulleys out of alignment inward toward each other - a big no-no.
My passenger's side camshaft had a little bit of spring action in it - when I had it all installed, the pressure on the water pump pulley would pull it about a tooth clockwise inward toward the water pump pulley - but then when I pulled the pin on the hydraulic tensioner to take up the tiny slack between the passenger side camshaft pulley and the crankshaft, it pulled it back into perfect position.
Also remember that the important thing isn't to get the BELT marks to line up exactly (they should, but that doesn't mean a lot... the belt itself can be anywhere along the rotation cycle so long as the camshafts and crankshaft line up with their marks and stay there), but rather to make sure the marks on the CAMSHAFT sprockets line up with the dots on the back timing belt cover, and then keep them that way. The marks on the belt simply serve as a good guide to make sure the other two are lined up with each other and you generally have taken up the slack in the right places. Don't let any of your 3 sprockets move, but the passenger's side pulley may turn just a fraction of an inch during the final belt installation to the exact same degree that it will rotate back when the hydraulic tensioner is installed. Pick a tooth or two on each sprocket and use a marker if you have to in order to get a good reference point between the sprockets and a fixed point on the engine, and use binder clips from an office supply if you need to get the timing belt to keep its teeth down on the camshafts while adjusting.
1994 Rodeo 3.2 SOHC V6, 5-speed Manual, 180K miles+. Rotella Syn 5W40/PureOne.
1997 Trooper 3.2 SOHC V6, Auto, 4WD, 135K miles+.