Ok, heres a copy, with dimensions, of the reg mark I was talking about. The width of each leg wants to be .013". You put one of these in each corner of the rectangle that bounds your print. They MUST be square with each other.
The light pen is easy, try this...
Load some media, any media.
Select, say, condition 2 or whatever condition you want to use.
Press the Conditions key
Press the F4, Offset, key
Press either the left or right arrow until the pen says 'light point'. It should start saying something like 'CB09Ux' which is the standard blue pen holder blade.
Press Enter.
Now that condition number is set to use the light point instead of the blade. You can select that condition to use anytime you wnat to use the light point instead of the blade.
If the software fails to detect the auto reg mark that is printed you're pretty much out of luck. There is a way to save it if and only if you know EXACTLY the size of the rectangle of which each reg mark is a corner. Other than that, there is no way whatsoever to salvage a job that craps out reading the auto reg marks.
Alternatively, you can specify to use the 4 point registration marks and manually set all 4 corners. On the Rip and Print Advanced tab invoke the 'Contour' button and select '4 point' from the menu of registration mark types. It should be the first one on the list. This will print a little bombsight looking thing at each corner of the print. When you load the print in the plotter to cut the contour job and send the job to the plotter it will ask you if you want to do interactive or digitize. Chose digitize [bombsight]. It will ask you if you want to use the light point, select 'Yes'. with the plotter's arrow keys move the media and the carriage until the light point is dead nuts centered on reg mark #1 [they're numbered 1 thru 4]. When you get it where you want it, press Enter or whatever its called on the dialog on the computer NOT on the plotter. The software will move to where it thinks mark #2 is. Using the plotter's arrow keys you move thing until the light point is smack dead center on mark #2, 'Enter' on the dialog once more. Ditto for #3, adn #4. Then the software will tell you to replace the light pointer or something like that, just select whatever means 'Continue' on that dialog, you don't have to physically change a thing, the machine will use whatever condition you've selected. The plotter will take off merrily cutting the contours. If you were accurate in your positioning, it will be right on the money. Hint: Set the disposition of the cut job to 'hold' instead of 'delete'. Then, if you should need to restart, like you wanted to select the light pen to see if all was correct, you can resend the job using the blade when you're statisfied with the setup. You'll have to re-register the job every time, that's the penalty for uncertainty.
But, back to doing it manually...
What you're doing is forcing the print to be located between the registration marks that you manually created. You use the plotter's, NOT the software's, automatic regstration mark sensing apparatus to let the machine set and deskew it's own plot area from the marks you printed. Once it does that the origin should be right at the bottom right point of the bottom right registration mark. Once that's done, it really doesn't matter about the other three registration marks, everything will be relative to the origin. The you send the contour lines as a plain old cut job. If the print is properly registered and and the bottom right reg mark on the print is the bottom-most and right-most object on the cut, the contour will cut perfectly. That's why you want to set a 0 margin for the panel as well as set the location of the cut to be the right side, not in the middle, not moved either up or to the left.
I do this all the time, most every day, and since I went to this method I've never had to toss a print away. It takes a little more forethought to set the job up for this sort of manual registration, but you never lose.
If any or all of this is still not clear I understand, this is one of those things that it's far easier to do that to tell someone how to do. If you like, PM me and I'll tell you how to get hold of me and I'll try to talk you down.