I don't remember a huge problem doing it, but make sure you're using the correct bolts, which should have a pointed tip to help line them up, and then try inserting just one, close enough to tight so that the box pivots on that one bolt without flopping sideways. If the box is wobbling all around, it will be hard to get the second bolt in without crossing the thread.
If you're having trouble getting even the first bolt in, another trick that might work is to find a couple of very long bolts a couple of sizes too small, and simply hang the box on those to take some of the weight off. Now you can hold the box with one hand and feed the first proper bolt into the remaining hole with some hope of getting its threads engaged right, because you're using your strength mostly to wiggle the box around, rather than trying to hold it up and align it at the same time.