The article about putting the mtx system into your atx won't help you, it will just confuse you.
To put a 3.2 into your mtx:
Remove all of the accessories and accessory drives from the 3.2 and 3.0, as you are going to install all of the 3.0 stuff on the 3.2 before you put it in the car. This includes the timing belt idlers and covers, including the metal rear timing belt cover. There will be some grinding needed on the front head to get the metal timing belt cover and alternator to fit - this will be apparent as you try to do this. All of the bolts for the timing covers will not line up, but enough will to secure the covers. If desired, you can drill and tap holes for the last 1 or 2 bolts.
You can swap in the 3.0 intake cams, but this is not required. If you do, you will only notice a difference above 4000 rpm. The 3.2 additional torque will be noticeable, even w/o the cam swap.
After you put on the timing belt covers, you will see a gap of ~1"x2" where the 3.2 oil pump leaves a gap because its smaller than the 3.0 pump. It is preferable to keep the 3.2 pump and fill this hole in some manner (some JB Weld and a piece of plastic, for example).
Remove exhaust manifolds, and put the 3.0 manifolds on the 3.2.
Remove the flex plate and flywheel, and install the flywheel on the 3.2. The cranks are identical. The flywheel is oriented with one of the attaching bolts being not equally spaced as all the other ones are.
It is preferable to swap the oil pan. The advantage is that it keeps the low oil sensor in the right location and keeps the Y-pipe holder, so if your 3.0 pan doesn't have a hole punched through it, that swap is recommended.
The 3.2 at this point looks virtually like a 3.0 from the outside, and the 3.0 motor mounts are used exactly as they were on the 3.0.
I know I left out some details, but that is the gist of it. Hope that helps.