It might be an obvious answer and I also haven't looked under my truck yet but the thought just occurred to me.

If I was to have a flat on the side of the road where should I place the jack with my running boards? Am I still able to get to the frame under the running boards or should I jack from the front/back of the truck?

 

You should still be able to get to the frame.

 

somewhere on the frame....depends on how and what kind of jack you'll use though....

 

You'll be able to get to the frame no problem with your boards there.

I've had 2 set on my truck before getting my Amp steps and always jacked from the frame.

 

It's the standard jack that comes with the truck.