I usually hand thread the bolts until lightly bottomed out, then back off slightly. (You can strip the aluminum threads in the flywheel if the bolts are too shallow, and they twist a bit in the process.) In any case, make sure the puller is square to the flywheel when ready to pull. Use washers under the heads if the bolts need to be adjusted to get them even -- likely want to use washers anyway to make sure the bolts fit securely in the puller (thinking of a steering wheel or harmonic balancer puller, and maybe less than top-of-the-line.) Leave the loosened flywheel nut in place on the top of the shaft to protect the shaft. Tighten the center bolt by hand until everything appears to be square and even, then crank the bolt down tight with a box or crescent wrench. Whack it once or twice with a two-lb hammer (my preference), then crank the bolt down a bit more if the flywheel hasn't come loose. Repeat as necessary.
The nut on the shaft will keep the flywheel from fully coming off, but it will pop with some force -- sounds like something broke if you haven't done it before.
