I will be traveling to Zurich and Germany in Sept. I haven't decided if we will be driving or traveling by train. If we travel by car, will there be any difficulties crossing the border from Switerzerland-Germany? Is there a border patrol and if so, what documentation should I prepare to show?

The Swiss still have borders and will charge a fee for a sticker to drive on their "interstates"
If you have a MC (Motorrad) licence and are on a bike, you may get away without charge.
M

Depending on the phases of the moon, the road you're on, what's on television that night and how close it is to shift-change time, you may find the border unmanned, you may be waved through without stopping, they might have a quick look in your boot to see if you're loaded with explosives, or anything in between.

Have your passports out (it's really, really lousy manners to other road users to keep people behind you waiting while you fumble), and know where the insurance document for your car is.

Generally, borders are about as big a disruption as a moderately busy road junction.

FlannerUK is correct. Just make sure you have your passports and car insurance card (I think the green card) available. Chances are they won;t bother to look at it - but they may - and its impossible to tell in advance who they'll check and who they won't.

If it's an Autobahn border, you will have to pay there and then if going into Switzerland and don't have the sticker.

flanneruk's post catches the essence. I've had experiences with having the car searched fairly thoroughly and being waved through without bringing the car to a stop. On smaller roads, don't blink, you might miss the border.