The problem I see is that as new cameras come available, CS6 may not handle the raw images, so you would have to convert to the Adobe raw before using CS6. Since you have CS5 you can probably still get CC and LR for 9.95. Since CS6 is the last photoshop you can own,it is a tough decision. I am using CC (and own cs6 and Lr5) and trying to decide whether to continue with CC. It already has some features not available in cs6. At 9.95 it is not much more expensive that upgrading CS and LR. I do not use cloud storage, because I don't trust it.
There are lots of choices. I do mine by date (2014xxxx). Within the folder I type the name of the subject/area/whatever and renumber the images (otherwise you can end up with two images in the same folder with the same numbers if you have had a good day). Other folks name the folder by location, or subject matter or whatever. I use the date because with nature photography I tend to remember dates when I was in a particular location. I can then use key words to identify subject matter (elk,bear,whatever). I HIGHLY recommend Tim Grey's Lightroom, etc, instruction which can be found herehttp://greylearning.com/join.html
It will be the best $50 you have ever spent. He has lightroom, photoshop, photoshop elements, Nik, OnOne instructions (and others) and for the $50 you can download all of it. He devotes a good bit of time to naming folders in Lightroom. He has about 8 movie downloads devoted to Lightroom, most of them in excess of 1 hr viewing time. Since you are just starting with lightroom, this would be the best place to get information from a really great instructor.
Why would you not be shooting in raw? The different "scenes" only effect jpegs. With jpegs, some guy in Japan or Korea or wherever is deciding what the scene should look like (built in camera software) and that person has never seen your subject. Relatively inexpensive software (Lightroom) is very easy to learn and does a very impressive job with the raw images.
I carry mine over my shoulder with camera and lens attached. The only reason I hike is to photograph nature/wildlife, so I don't have a backpack. I carry extra lenses in a belt pack from Think Tank to get the weight off my shoulders/back.
You are already covered from 100-300. It would make sense to me to get a prime 400mm. Canon's 400mm f/5.6 lens is one of the best for bird photography. It is faster focusing than most, especially IS lenses. For birds in flight, I find IS to be of marginal (if any) value.