In the first case where a comma should precede the Year, it sounds like the comma might be missing from the Citation template of your output style:
1. Go to the EndNote toolbar, select Edit > Output Styles > Edit [name of the output style you’re using]. This will display the output style’s main screen.
2. In the left column (see attached image), click to select “Templates” which is listed just below the “Citations” section. Insert a comma in the template as shown.
In the second case (where a comma should not appear after “et al.”) could you clarify your example which seems to imply using “et al.” involving two authors? But assuming “et al.” occurs in the case of three or more authors and as specified by your discipline’s style guide it sounds like a comma might have been included in the Abbreviated Author Lists section of your output style:
3. In the left column (see attached image), click to select “Author Lists”. Examine both Abbreviated Author Lists sections and delete the comma appearing after “et al.”.
4. Close the output style which saves the changes as a new output style with the word “Copy” added to the file name You will then need to change MS Word and EndNote to use the new output style changes.
Can you provide the publication that requires the different handling of the comma after Authors names as opposed to et al.? In my opinion, that is weird. (I am often accused about being OCD on these kind of things, and I would leave it et al.,)-- and I suspect they have an in-house mechanism to fix it, if they really care.