If you are using a flex cable for throttle, it shouldnt make a difference wether the engine is upright or inverted. As to the front or back line being up, it does make a difference. If the elevator control horn is above the elevator, then pulling on the rear line will make the plane dive. If it's below, it will make the plane climb. It's usually below, but you need to look at the side view of your plans and order acordingly.
Yes, you can taxi, but as you have guessed, it isn't easy. Like I said before, electric controls are much easier to use.
Don't worry about asking questions. Us old farts just love to give advice.
Steve