Based on the length of my reply, I obviously have too much time on my hands this evening.
But there is no brief way to answer your question. Don't let this scare you away. It's not as bad as it looks. Don't hesitate to ask further questions.
Initial suggestion: Since you have an external enclosure, I strongly recommend that you put your new SSD in it and format it there and install El Capitan on it there (I assume you know
how to select an external drive in the OS X installer). Doing the formatting and installation in the external enclosure could save time because Disk Utility doesn't always recognize unformatted SSDs when they are in the computer itself. After El Capitan is installed on the SSD, and the SSD is then installed in your MacBook Pro, it should start up without any problem. If there is a problem, hold down the option key to select the startup drive that way. After the new drive is installed in the computer you should change the name of your old hard drive
from "Macintosh HD" to something else, and the name of your new drive
to "Macintosh HD." This is only to prevent confusion.
When I plug the old drive in via USB, what will the file structure be like...
It will look exactly the same way it does now, although two or three formerly invisible folders may become visible at the root level. It's no big deal.
and will there be anything locked?
This has been inconsistent for me, but, generally, nothing has been locked FOR ME in recent years; however, if you want to be totally sure that nothing is locked, use the very same OS X username(s) and password(s) that you are using now when you create your new El Capitan user account(s).
How do I transfer apps (along with user profiles) to the new apps folder? Are there ones that won't do so via drag and drop (I know many newer apps have an install process rather than simple dmg>drag/drop)
There may be easier ways to transfer files, but I am either unfamiliar with them or don't have full confidence in them. The following is how I've been doing it since the 1990s. To be as safe as possible you should keep your old hard drive in the external enclosure for several months without erasing it or deleting anything on it. That way, if you inadvertently leave any files or system preferences behind, you can always go back and retrieve them.
1.) Put any and all files located on your present desktop into a single folder called "Temp Desktop Transfer" (or whatever name you desire). This will help you to feel confident that you haven't missed anything (no "clutter" equals less confusion and doubt). Then drag that single folder to the SSD's (El Capitan's) desktop. Back on the old drive again, turn that "Transfer" folder Red to indicate that you are done with it (or add the word "DONE" to the title).
2.) Open every remaining folder in your Home folder (Documents, Movies, Music, etc.), one at a time, do a "select all" and transfer the files to the corresponding folders on the new drive. Turn each folder (Documents folder, etc.) red on the old drive when you are done with it. Save the Library folder in the Home folder for last.
3.) The Library folder in the Home folder is more time consuming. You will just have to use your intuition / common sense on what to transfer right away and what leave behind for a while or forever. Open the old and new Library folders side by side to make comparisons of the files in each folder. The most crucial items (for me) are in the Application Support, Fonts, Mail, Mail Downloads, Preferences and Safari folders. Of those folders, only the two Mail folders should be transferred in their entirety (meaning drag
the folders themselves to the same location on the new drive).
HOWEVER!!! If your email account is IMAP instead of POP, you don't need to transfer those folders. But, if you have a combination of POP and IMAP accounts, then you need to transfer them. The rest of the folders you will need to open and pick and choose the desired files. In the Safari folder, you should transfer ONLY the "bookmarks.plist" file and the "history.plist" file. Don't transfer anything else, including the Safari extensions files. Reinstall the extensions the proper way. Ignore the Caches and Keychains folders. Transferring the "login.keychain" file can cause very annoying problems. I may be wrong, but you will just have to reenter your passwords one by one, as you need them.
4.) In the Preferences folder, you may ignore many of the files that begin with "com.apple," but you should definitely transfer all "com.apple" files that are associated with iTunes, iPhoto, Mail, Messages, Facetime(?), Safari and any other Apple apps that you use, not counting Preview or TextEdit or any Finder or other system preference files. Turn each preference file red on the old drive as soon as you have transferred it, so you don't forget what's done and what isn't.
5.) Applications folder: Reinstall all 3rd-party apps using their installers, if you have them. Transfer the remaining 3rd-party apps manually. iPhoto will almost certainly have to be transferred manually and then updated to 9.6.1 in a very convoluted way, thanks to Apple (ask me how when the time comes).
Side note: Do not open iTunes on the new drive until your iTunes Library folder has been transferred to it. Even then, as a precaution, you should open iTunes in El Capitan the first time with the Option key held down. Then click the Choose Library…" button to locate your iTunes Library. In the past, iTunes often created a new, empty library, instead of finding and opening the correct library, if the option key wasn't held down. I don't know if that's been fixed or not.
6.) Regarding the Library folder at root level of the Macintosh HD: You will have to use your intuition/common sense and/or ask me questions about specific items. The Application Support and Receipts folders have a lot of important items in them, though.
7.) If there are other OS X user accounts on your computer, you will have to log into each of them, one by one, in order to transfer their files to the corresponding new user accounts on the new drive.
If you have any more questions, just ask. I've got some free time on my hands.
