Im a little late to the party by 3 months....
...but have you seen this laser tool for non-laser eye cutters?
eBay Express: Vinyl Cutter Contour Cutting Laser alignment tool sign - Description
Ive never tried it but was researching the same question the OP asked a while back.
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when I need to contour cut on a non-lasered cutter I do basically what lnfortun mentioned:
I print out the image(s) on the vinyl, paper, poly, etc. I also print 3 registration dots outside the images I am trying to contour cut. The reg dots basically form a large "L" shape outside all the image(s).
After printing I bring it over to the cutter and pop a pen into the knife holder. In the cut software, I simple move the L shaped cut lines that connect the reg dots to their own layer. (these "cut" lines will be traced by the pen, and not actually "cut" -- just used to get the registration all honkey dorey)
I then spend a few minutes getting the substrate alignment correct in the cutter's rollers so that the pen draws the L shape perfectly, connecting the reg dots. (perhaps on this step, if you had the laser in my link above, you might not need the pen???)
Once youre perfectly connecting the dots, then swap the pen back to the knife, switch layers in the software to your contour cuts, and let 'er rip.
This usually works perfectly fine for 95% of what Im doing. Not perfect alignment, but I find I can cut to easily within 1/16" to 1/8" of the actual lines. Sometimes I get lucky and nail perfect alignment with it -- maybe 20-25% of the time that happens. The largest area Ive attempted this technique at is 13x19. ( largest size that can be spewed from a epson 1400.) I don't do this often, but it does work when I need it.
To compensate for the slight offset errors using this method, I usually just overprint my 'bleed color' 1/8" larger than the contour cut size. I.e. I print slightly outside the contour lines by 1/8" all around. Close enough for Rock n Roll in my book.
Im sure there are better ways to register w/o a laser eye, but that was what I can up with in a couple of hours of farting around with it.
As noted, this is really the same thing lnfortun/Luis has aleady described above in the last paragraph of his reply above. Just a bit more detail to the process is all.
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Ive also applied a temp backing to stuff I wanted to cut that is only single layer but that the machine can cut through. YOu know, just "die cut" objects. For example paper cutouts with no printing on them. I just tore off some vinyl from it's backing and used that as the paper backer and stuck the paper down to it. Worked fine with a extremely light mist of spray glue on the paper.
PS: mods should probably move this thread over to "vinyl cutters" for indexing purposes. I'd probably never search the heat press forum for cutter related posts
contour cutting w/ no eye 
MAD Scientist JR. AKA MS2
