I see a basic problem with transistors that people must have figured out how to deal with I just don't know what you're supposed to do about it. When using both pnp transistors and npn transistors, the arduino will be hooked up to the emitters (or maybe collectors I can never remember which is which) on both the high side and low side. What I mean is like when you use a transistor with an arduino you have to connect it to ground on the arduino, likewise when you use a pnp transistor you have to hook it to the 5+. This isn't a problem when using just one of the types but it seems like if your trying to control something really high voltage with pnp and npn transistors the arduino will be exposed to it, defeating the purpose of using the transistors. I'm just a bit confused conceptually
That's why people go to college and study to become electrical engineers, so they can figure that all out. 
Seriously, there is no short cuts to learning fundamental electronics, and then on to semiconductor principles to be able to design circuits that work and don't burn up stuff. and until one gains such knowledge and experience, it's best to copy existing proven circuits in your projects.
Lefty
One typical solution is to the PNP high-side voltage problem is to use another (NPN) transistor to switch the base voltage for the PNP.
Thanks thats what I was looking for 
A further comment - when controlling high-side things from the low-voltage part of the circuit you usually control a current, not a voltage. At the high voltage end a resistor converts that current back to a voltage relative to the +ve rail. For large voltages opto-isolators are often employed.
KE7GKP:
Take "low-side switching" and "high-side switching" as separate cases.
Heck, if I've heard those terms before, I don't recall. So I did some searching, and found a couple tutorials. Now I've learned something new!