What I do first when confronted with a big collection of photos is to get some kind of organization scheme. I try to sort by family branch (distant relatives may be one pile, grandma's photos may be another). I then arrange chronologically. Since it's impossible to exactly date a lot of photos, I group them by decade. I keep photos of events together (Christmas with aunt Martha, trip to Oregon, etc). If the back is blank, I often pencil in the year and place. I also add in a index number to each photo in a group so that if they get mixed up, I can re-sort them quickly
After I've organized my photos, I then cull a bunch of them. I don't throw them away, but I figure out which ones I'm not going to scan. I don't have time to scan thousands of photos, so I pick a representative sampling of each event or from each branch of the family. I just don't need to scan a dozen photos of my mom's tulips, no matter how proud she was of them. One is fine.
Once I have stacks of sorted photos, I start scanning with the first.
Placing Photos on the Glass
I've learned a thing or two about placing photos on the glass.
The first issue is that a few millimeters are cut off when photos are placed against the plastic edge on the side of the glass. This is unfortunate, because it's easy to make sure your photos are straight if you place them against this edge. If it cuts off a part of the photo you don't care about, such as the border, then it's okay. But if it's a historic photo, then you may wish to place it away from the edge a few millimeters.
Which brings up the second issue I've learned. Placing photos on the glass so they are straight is hard to do! What I learned to do was hit Preview in the scanner software with the lid open. I then readjust and hit Preview again, until I'm happy with how straight all the photos are. At which point, I carefully close the lid and hit Preview one last time.
Another solution to crooked photos is to use a software function to straighten the photos after the scan. This function is called anti-skew, and it is much quicker than physically straightening the photos. However, according to the article How To Properly Scan a Photograph by Eric Goodnight on HowToGeek.com, this can lead to smeared pixels and a loss of resolution. I can believe it, since an anti-skew algorithm would have to ever so slightly modify every pixel in your image to correct for skew. I'd rather straighten the photo physically and not worry about the tiny loss of detail.
Of course, if you have hundreds of photos, using automatic anti-skew may save quite a bit of time.
Naming Scanned Photos
An excellent system for naming scanned photos is explained in the article What Everybody Ought to Know When Naming Your Scanned Photos by Curtis Bisel on ScanYourEntireLife.com. I concur heartily with this naming system. It's well thought out, and you can definitely figure out what the photos are simply by the long descriptive names.
Basically, the article suggest the following format for names:
Date + Description + Scanner Settings
I strongly recommend reading the article for the details of this system.