The bottoms of the forks below the fork boots swivel, so the axle will line those up. The manual says to have 6 MM (confirmed, just looked at the manual) of fork protruding from the upper triple clamp. I used a bolt, a couple of washers and a nut to make a measuring tool. I laid washers on the bolt until I got it the same height as what was prodtruding from the upper triple tree and then I put on a nut to hold it all together.
To add too what Rainman has mentioned, I have some photo's in my "A TW without Forks is Like a Duck without a Bill" thread that may be of some visual assistance. Though not a step-by-step process, I replaced a buddies fork boots and seals. Later today I will post some of the photo's from the actual fork seal work, though you only mention the boots.
But as Rainman has mentioned, fairly easy to accomplish. I can see where someone would be a little worried about taking the forks off and putting them back on correctly. Once you get started, replacing the boots should only take an hour or two (depending on the number of interruptions) giggle.