Thank you for your interest in our laser cutting, and for bothering to ask these questions! We do plan to address these issues more clearly on our web site; it sounds like you already looked at what we have up for now in our online documentation, but in case you didn't notice that there are many sections, here's a link to the entire laser cutting guide on one page:
I'll specifically answer your questions, but I also want to generally address the topics you brought up (since we do get similar questions often!):
FILE LAYERS for laser cutting:
In general, putting all cut lines on a single layer is the best for our process. We do prefer that you use a second layer for all of your annotations and a third layer for your engraving, but we can work with annotations and engravings on the same layer as the cut lines as well. All layers should be unlocked and editable. Please delete layers that aren't needed (do not make them invisible). These layer restrictions are only to make it easier for the person preparing your file for laser cutting and quoting; the more closely you follow our guidelines, the faster we can provide a quote and cut your parts.
SIZE REFERENCE in laser cutting files:
For every laser cutting file you submit, please do include some type of size reference. A 1-inch square (or 1-cm square) labeled, "1-inch square size reference" would be great. We will not include the size reference in your final cut or in your PDF proof unless you note otherwise in your quote request.
ANNOTATIONS/SPECIAL INSTRUCTIONS/PDF PROOFS for laser cutting:
Somebody always processes your original files and makes a version of it that is optimized for quoting and for laser cutting, so you don't have to worry that we will accidentally cut and charge you for the annotations in your file. You may include various annotations and text in your files, and we also provide you with a text box in the online quote system for special instructions. If you like, you may also call us (702-262-6648) and ask for the laser cutting department to discuss your quote request (you could even note, "please wait for my call before you process this quote request" in your special instructions).
Once you submit your quote request on our web site, somebody will process the request and email you a link to the quote, which will include a PDF proof of what the quote is for. If you want to order the quote, you must approve the PDF proof, first. If you notice something wrong with the proof (if there is engraving text missing, if there are annotations that we misunderstood to be engraving, if there aren't enough of part X, etc.), there is a way for you to disapprove the PDF proof and explain how to fix the problems. The quoter will fix the problems and the cycle starts again.
SAVING INSIDE CUT-OUTS of laser-cut parts:
If you want us to ship the inside cutouts, please note that in the "special instructions" section of the quote request. If your request is somewhat complicated ("keep this one, but not that one"), you might consider using different colored lines in your file to indicate the cutouts to save, and to note, "save all cutouts drawn in magenta".
HOW MANY FILES for laser cutting?
Please submit one file per material. In your case, you would submit two files. Note that your quote should have two of what we call, "designs": add one design with one file and material, and follow that by adding a second design with your other file and material.
Here's a more comprehensive example: If you have 20 parts to cut from 3mm clear acrylic, part X to cut from 6mm clear acrylic, and also part X to cut from 3mm black ABS, you would have to submit a quote with three "designs":
design 1: one file with 20 parts to be cut from 3mm clear acrylic
design 2: one file with 1 part (design X) to be cut from 6mm clear acrylic
design 3: one file with 1 part (design X) to be cut from 3mm black ABS
You would probably submit the SAME FILE for designs 2 and 3 unless you have different annotations in the the two files. It is helpful if you note something like, "design 2 and 3 are the same part, but just from different materials" in the "special instructions" section of your quote request.
Your file for design 1 might only have 4 different parts, with annotations explaining how many copies of each part you need (e.g. "2 of part A, 6 each of all other parts").
I hope this helps!