WINE is, as you said, an implementation of Windows APIs for *Nix systems. That means that it only runs programs that you directly tell it to run. The basic syntax for WINE (once it's installed of course) is
wine programName.exstension, so if you wanted to run Evernote 188.8.131.5242, then you would
cd into the directory that Evernote is in and type
wine Evernote_184.108.40.20642.exe to run it.
What this essentially means is that any windows malware needs to be executed to work, so if you download a corrupted version of someProg that in turn downloads and executes someMalware, then nothing would happen. The reason being is that instead of executing someMalware like Windows, for the malware to work it would need to be initiated by WINE, and therefore by you. Installing WINE does not open your computer up to any "Windows malware" because you are directly in control of what exes, bats, and coms WINE executes. The only theoretical danger is if you download a Linux program that downloads a windows virus, and then calls WINE to execute that virus, and then fixes everything to work out of the WINE sandbox.
In the long run, your Linux computer is completely safe with WINE. The only real danger is what you install, which in your case is Evernote. If you get Evernote off of the official site and just run it with
wine Evernote_220.127.116.1142.exe (if it's that version), then you will be completely fine.