If you've got the converter and engine out, you can line up the bolt holes (and mark them) before installing it. Otherwise it's just trial and error... Bolt up 3 bolts, see if the last one goes in easily. If not, spin it around, pull out all three bolts, move it to the next hole and start over.
If you've got luck like me, it'll be the 4th combination that you try.
DONT force the bolts in, if they don't go in easily it's not lined up properly.