Pronterface not printing on Prusa in same location

Hello Everyone,
I have just finished building my first Prusa and am having problems getting the position of objects to print on the bed at the same location I see it in pronterface.

Here is what I am using. Splinter Firmware on RAMPS 1.4 with Slic3r -> Pronterface.
The recommended settings in Slic3r for the Prusa is a 100cm 100cm center point. When using this is seems to think the center of the build platform is in the far bottom right. Also, the object is printed 180 degrees rotated, kinda like "upside down".

Is there a procedure that I need to perform to make the machine aware of the real dimensions of the print bed? I would like to do larger builds but I am afraid of stepping too far in one direction.

I have a ABSPrusa mendel. With the thing on the desk with the Y axis motor nearest me, I have it so that the XY home is in the bottom left corner. Increasing X goes to the right. Increasing Y makes the bed move towards me.This is the correct orientation for XY wrt Z. So, with the end stop sensors on the X and Y placed so that this is home, you may need to swap two of your X stepper wires and/or two of your Y axis stepper wires so that pressing Home makes the head move to this position.

X axis end stop sensor is on the left and I've put my Y axis end stop on the smooth rail at the opposite end from the Y motor. I atually moved the smooth bar through its clamps away from the Y motor to give me enough bar on the outside of the clamp to attach the sensor.

I use Sprinter firmware and in Configuration.h you need to set the travel limits. By the time I take into account the clips that hold my bed together, I get 180mm by 180mm with a center of 90,90. This info also needs to be entered into SLic3r in the Advance tab.

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Using ABSPrusa Mendel Zaphod with Pronterface and slic3r 1.3.0. Printing well with 3mm PLA and ABS through 2 x J Head Mk IV b and Wade Geared Exruders. Controlled using RAMPS1.4 board running Marlin_v1.1.9