I do the same thing as Ella when it comes to labeling mylar. It is really the only time I use a Sharpie or non-archival pen. However, I have also written on an archival sticky label (http://www.gaylord.com/Archival/Conservation-Supplies/Labeling-%26-Marking/Gaylord%26%23174%3B-PermaPlus%26%23153%3B-Paper-5-16-x-1%22-Laser-%26-Inkjet-Multipurpose-Labels-%284%2C550-Pack%29/p/346L25) with an archival pen and then put the label on the upper corner of the mylar sleeve. I have found both methods to work well.
As far as digitizing while in the mylar sleeve, I have found that when using the scanner it is no problem at all. I actually prefer to have it in the sleeve when scanning because it add stability. That being said, I have not had good lucky photographing a document while in the sleeve because of the glare.
I use the double sided 3M tape from Gaylord (http://www.gaylord.com/c/3M%26%23153%3B-415-Polyester-Double-Sided-Tape-%2836-yds-%29/p/HYB00644). If you try making the envelope slightly larger than the object, thus allowing for a little wiggle room, it does not come apart. This is especially true if you are putting multiple pages in one sleeve.
Hope this helps!