How do I use a new tnsnames.ora? Can I use multiple tnsnames.ora?
This isn't really a Toad question, it's more of an Oracle question, but I'll answer you.
If someone gave you a new tnsnames.ora file, you can do any of these with it:
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manually merge it with your existing tnsnames.ora file. They are text files that you can edit with notepad
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use an ifile command in your existing tnsnames.ora file to include it.
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replace your existing tnsnames.ora file with the new one.
You can also have a separate tnsnames.ora file for each Oracle client that you have on your PC, but I feel like this is unrelated to what you are asking.
Which directory should the tnsnames.ora file be stored in?
Thank you 
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Check out the Oracle docs for tnsnames.ora. It covers the location, IFILE, etc. Local Naming Parameters in the tnsnames.ora File
The easiest thing to do is make an environment variable named TNS_ADMIN. Set its value to any folder path you want. Place your tnsnames.ora, ldap.ora, and sqlnet.ora files in that folder. That's what I would do if I wanted all of my installed clients to use the same config files.