just wondering about how everybody lines up the rear end after having wheel off and some of the suspension

Measure the distance between the axle and the swingarm pivot bolt on both sides. Once I know they are the same, I check the stamped marks to see if they are correct.

I borrowed a tool from a friend that is a machined aluminum clamp (clamps on the sprocket) with a steel rod pointer that parallels the chain.  Line up the pointer with the plane of the chain and you're set.  The tool costs about $25 at a cycle shop.

FWIW, my factory alignment marks were right on.

Hi there,
That "chain alignment tool" is made by Motion Pro and I love it.
The chain adjusters on our GS500s are a lousy design, but this tool makes it a lot easier to get everything lined up correctly.
I've found that the stock adjuster marks on the swingarm are not accurate, so this tool is a big help.
Here is the tool from the Motion Pro catalog:
http://www.motionpro.com/motorcycle/tools/chain_alignment_tool/
I highly recommend it as well.
Best wishes,
Todd

I4

In a word "Practise".  From the rear of the bike crouch down and look along the top and sides of the chain. If the wheel is out of alignment the chain will be kicking  over to one side where it engages on the rear sprocket. In effect its the method Trumpetguy is talking about but you can do it by eye without any  tools. After doing it several times and with practise you will get your eye in and be able to do it by sight. I dont use the scales on the swingarm, they are miles out on mine.

Hi Wrecent et al,
By using the Motion Pro tool, it means that the REAR SPROCKET, which is bolted to the wheel and hence part of it as a reference point, is correctly aligned to the countershaft sprocket when the rod on the alignment tool is aligned with the chain side plates.
The tool itself clamps around the rear sprocket, around the chain, and uses the sprocket to ensure alignment.
So yes, it does align the wheel.
It's cheap and makes it easier than doing it by eye alone.
That's why I like using it.
Best wishes,
Todd