I could write a book!
But I jest.......... 
1] About setting up accounts in Thunderbird:
Yes I think it would be preferable to remove the tick in the "Use global box" option to store emails in the "Local Folders" list. Giving each email account it's own set of folders, (called directories by Thunderbird, but that is now an outdated term in Windows), is the general practice I believe, and that's certainly what I do.
This is what happens with me and Thunderbird with my email accounts. When I open Thunderbird it automatically connects to my broadband ISP and downloads any email messages from my main account. The other accounts I have set up in Thunderbird do not automatically download emails. Only when I click the small down arrow next to "Get Messages" in the toolbar, and select "Get all messages", do the other emails arrive. They are distributed into the separate Inboxes for each account.
If you have already set up these email accounts in Thunderbird to deliver to the global folder, that's not the end of the world. You could set up new sub-folders, (perhaps call them Inbox-{2nd account name}, Sent-{2nd account name}, Trash-{2nd account name}, Inbox-{3rd email name}, Trash-{3rd email name}), etc, then set up "Message Filters" in Tools > Message Filters to divert emails from other accounts to your new sub-folders. Or, if having a global Inbox works for you, then that is fine.
In Tools > Account settings > and the Server Settings for each account, I would set the following settings;
"Check for new messages at startup", (of Thunderbird). This tells you immediately how many emails you have ready for each account.
For your main account, "Download emails automatically", but not for the others. This lets you delay downloading other emails until you're ready.
Leave the options to leave messages on the server blank for all accounts. If messages are left on the server, they tend to get forgotten about, build up, and then the account admins get concerned.
"Empty Trash on exit". Empties your trash for you.
The option to check for new messages every ? minutes is up to you.
A word about using one ISP to check for emails from other accounts. There is a gentlemen's agreement between account administrators that one ISP can get the emails from other account POP servers. But sometimes the agreement doesn't exist. If you come across that, all you can do is connect to the other ISP and then start Thunderbird to download those emails. For example, I have 3 ISP's. My main is a broadband account but I also have 2 dialup backups for whenever my broadband goes down. I can download emails for all three accounts using any of the ISP's, but if I couldn't, I would have to logon to one to get those emails. This is generally not a problem with web based email accounts.
2] Safe email accounts.
This is tricky actually, because there is no real way to keep email accounts safe from all spammers. Some always get through. Also, there are two aspects to consider. Anti-spam and Anti-virus. For anti-virus your anti-virus scanner should be capable of scanning emails as they come in, and you should never open attachments without first saving them to the hard disk, (the Desktop is a good temporary area), and scanning them with the anti-virus before opening them. I don't trust any attachments, especially from relatives and friends. My friends and relatives tend to be less aware of malware problems than I am, and a few have virus and spyware riddled computers, despite my help and advice.
But back to anti-spam. ISPs block a lot of spam before it even gets to our POP servers. Some ISPs are better than others. I think we would be surprised how many they block. When I talk about ISP's, I mean ISP's that give us internet access, (and also one, or more than one email account), and web based email account providers.
Your ISP probably allows you to have more than one email account, and generally you can use any name you wish. You're right that email names are limited to alpha/numeric characters with the only exceptions the full stop and underscores, eg mark.flax@ isp.com or mark_flax@ isp.com. They are both common, and in fact some ISP's require a full stop. It's very difficult to think of an email name that is both recognisable to those people you want it to be recognisable to, and yet a jumble that will fool spammers. Indeed, spammers will use computer programs to create all different variations of names to send emails to. Most may be bounced back because the name doesn't exist, but that's just an expected thing with them. It's the ones that don't bounce back that they are looking for, and there is little we can do about that. The important thing for spammers is the ISP part of an address, eg @hotmail.com. The computer programs will send out anything to @hotmail.com, (eg fhskwow.dhdgs@hotmail.com as a jumble of letters), and if it bounces, so be it, but if it does not, then they have a valid email address. Spammers also like us to read their emails. There are tricks they can use that if an email is opened, they get to know, so they find out valid addresses.
If you want to see if your ISP allows more than one email address, visit their web site and search around for "Setting up email accounts", or similar.
We can help ourselves. If we have to give out email addresses, either use a throwaway address, or if we have to leave an address in a forum such as this, use the format mark.flax AT isp.com. Notice the AT instead of @ and the uses of spaces. Genuine readers will understand and make the necessary adjustment to mark.flax@isp.com, (not my real address), but forum robots that trawl forums for email address don't recognise the address.
Also, we can set up message filters in both email software and in web based email settings. These allow the emails to be downloaded, but they go straight to the Trash folder which is then emptied without being read, which prevents the spammers from knowing that the email arrived.
3] More resources:
Your best bet is to Google "Email tutorials", (without the quotes). You will get a whole load of email links where you can pick and choose. but you know, after a very short while, you won't need any tutorial or training. You will pick this all up as you go along.
Good luck and Happy Christmas.
Let me know if you have any more questions/problems.
Mark