Will my Aunt be offended if I ask her to sign an agreement about getting something of my grandmother's back?

You're all right... my mom's boss made me a copy and my aunt a copy and I really don't know what my aunt plans to do with the original... I will just ask her nicely to make a note of it. My mom printed the email conversation between her and my aunt I'm just going to save that and see what happens... I'm still going to put together a shadow box but I've rethought of how I'm going to.

Just ask her to put a note with it " Give this to Stargazerlilly" . Don't ask her to sign anything, it will upset the apple cart. Worse, it will trigger an avalanche of similar demands and leave your aunt feel surrounded by vultures.

I agree with Moxie1 about correctly storing historical documents in the acid-free paper, and that the orig doc shouldn't be put on display in a shadowbox (it should be in a safety deposit box!). And, there must be a reason why your aunt wants the original as opposed to a perfectly created document copy. In my opinion, a very nicely constructed photocopy should be enough for her, or you. I would try to find out why she thinks she needs the original, and why do you need the original? I know nothing is like a real original document, and I understand what the document symbolizes for you, but having the actual original document doesn't change the love that you have for both of your grandparents or the solidity of their marriage. And, I agree that you should have the marriage certificate willed to you if she is agreeing to give it back, but sometimes it not only takes money, but also takes time to change a will. My grandmother would not change her will for anything, even when she said she would because her son hadn't come to visit her in over 30 years, wouldn't call or stop to see her when he was in town, and didn't lift a finger to help in her end of life battle with fibromyalgia/COPD when she was bedridden...not a call, a card, or even flowers at the time of her death or even going to the funeral or offering condolonces. I hadn't seen my uncle in over 30 years and wouldn't know him from a stranger.

I would think a handwritten letter from your Aunt stating that the marriage certificate should be left to you in the event of her death (if she can't/won't add it to her will) would be sufficient enough to hold up in court should the document end up in someone else's hands. If your aunt truly wants the original marriage certificate to be in her hands only until she passes, and then return it to you upon her death, I think she shouldn't hesitate to write you a letter and provide copies of the letter for you and other interested family members.

Since it came from their temple, it is a church record and also valuable as a historical document. Please rethink the idea of putting it in a shadowbox where it will be destroyed by time. A high quality photocopy would be so much better to use in the shadowbox and could be replaced when it fades. Here is information about how to scan precious documents and photos:
http://presentationsoft.about.com/od/powerpoint2010/ss/110908-How-To-Scan-Pictures-And-Precious-Documents.htm

I'm sorry I should have clarified that it was from the Temple they were married in.

Its not the certificate they got from the state, its the one they got from the temple, so its actually pretty hard to replace.

I tired asking around on a few other sites and people are pretty much telling me that I need to have it left to me in her will.... so I guess I can just ask her to "will" it to me.
I just worry that it will end up to my cousins and end up in storage or something.

It sounds really stupid but my grandparent's marrige is the only marriage in my family where they truly loved eachother. My grandma spoke of my grandfather with pure happiness and love in her voice any time she would tell me about when they were "courting" and when they got married and their 49 years of marriage before he passed away... I guess to me, it symbolizes that there are people in my family who can have a normal healthy marriage where the spouse is not controling or always mean or getting in the way of family. I grew up with divorced parents so I've never seen a happy marrige except for my grandparents.

I don't think that a shadow box is an appropriate place for an original legal document such as a marriage certificate or family photos because over time light will fade the writing and destroy the photo images. These documents are often used genealogically and historically. A shadow box, while well intended, could damage or destroy the certificate or be discarded by someone who doesn't understand the true value of the marriage certificate. My suggestion would be that you make a high quality copy of the original document for the shadowbox. Alternatively, you could request a copy of the marriage certificate from the county clerk of the county in which the marriage took place. I truly believe that for a shadow box, a copy is the best and really only appropriate way to go. Preserve the original document by storing it in an acid free paper along with the family's legal papers. Here is additional information on how to store family papers correctly:
http://www.calarchivists.org/Resources/Documents/Brochure_Series/Papers_in-English.pdf

We tried that. She doesn't want the copy she wants the original. My aunt and mom are giving it to her and I will have a copy, and she said I would get it back, but I know my family, and I feel it would be best to have a signed agreement between the two of us that I get the orginal back

Why don't you consider getting a good color copy made and giving your aunt the copy now and you keep the original? Could you do that?? Talk to a local printer about it. There are also lots of photo restorers out there that could probably make an excellent copy so that you can both have one.