What is the best way to Texas Rig a tube? Do you run the hook in the middle or through bottom and out the top? Weedless?

Use an EWG hook (several companies offer tube hooks). Run the hook through the top (rounded end) and rig it just like a regular texposed/skin hooked plastic. The end result will look something like this and be very weedless.

A great tube to Texas rig is the Food chain tube from Power Team Lures, as the front 1/4" is solid so the hook set doesn't tear out the nose. Good pic showing the Texas rig too.

I either texas rig it like above or use a jig head.

The three most common methods of rigging a tube are T-rigged, with a tube jig, or with an internal weight which is similar to T-rigging except the weight is inside the tube rather than a bullet weight above the bait.

Tubes really shine when allowed to free fall as they will spiral their way down when the weight is inside. They are a great alternative to drop shotting or weightless stick worm presentations.

They are also dynamite as a drop bait  when rigged Texas style or with an external jig head.  My favorite for this is a stand up style jig that you can crawl along the bottom, or dead stick for inactive fish.