A course can only use one of LTI version 1.1 or LTI version 1.3. Typically, a single WeBWorK server will even only use one of those, but it is possible for the server to use both for different courses. LTI 1.3 is the newer and more secure protocol. However, it does take a little more work to set up. It is possible to set up LTI 1.1 without administrative access to the LMS. That is not the case with LTI 1.3.
Canvas supports both protocols (as do most LMS's now). If you have LTI 1.1 working, then go with that. It should be fine.