How will C+ and many B+ during online school affect PhD admissions?
The nature of the question suggests that this is in the US, so I'll assume that.
If your lesser grades are outside your major (math) and you otherwise have a good/great application including stellar letters of recommendation, then I think grades elsewhere will matter very little. Given the pandemic, even less.
Don't worry too much about it, but make sure everything else is first class. You can't do anything about the past in any case.