Currently there's no way to upload a Client SSH Key File directly in the SFTP connection to use. You have to put it on a local atom. There's a way around that uses the cloud work directory of your account though.
Please do not use the work directory to store things other than the SFTP key (or a few other small files) or store large files on it for use else where in your process. Dell Boomi might ask you to remove files if they are too large or many.
This is writing to the work directory, specifically making new directory called "samplefolder".
The message shape has the actual key contents. The set properties sets the file name, in my example I named it "test.key", you can name as desired. The Disk get is to double check the file exists. Using the test atom cloud will put the key file on the test atom cloud (you'll be able to test via test mode). Using the atom cloud (production) will put the key file on the production atom cloud, but you can only deploy and execute since you can't test with Dell Boomi production cloud atoms.
The root directory you can use is "work". If you want to use sub-directories, you can, remember to use the "Create Directory if it doesn't exist" option in the disk operation so it'll create it since there is nothing in the work directory the first time you use it.
Using the above directory and file name, the Client SSH Key File path would be work/samplefolder/test.key. You should be able to use the test atom cloud (test mode or deployed) or prod atom cloud (deployed) at this point to retrieve files.
To Walter Bissic and Stephen Harned for the information