The manner means "the way"
What you're saying is the "manner" of running a capaign, not the manner of holding elections (or "the way" you hold elections).Campaigns and elections are two different things. I think the "manner of holding elections", as someone stated above, is strictly the mechanics of it, which is, of course, covered by the USC and federal law.
And I may be wrong, but isn't the way one gets on the ballots governed by state laws?
CFR applies not to the election, but to the campaign. So it isn't covered by Art. 1 Sec 4.