Suppose I wanted to construct the spectral energy distribution (SED) of an object. Further suppose I observe this object through the 9 broad-band filters using the Subaru Suprimecam (just for an example) here: http://www.naoj.org/Observing/Instruments/SCam/sensitivity.html
As the statement below the table of broad-band filters says, the Johnson-Cousins filters (capital letters) are on the Vega magnitude system whereas the SDSS filters (lowercase letters) are on the AB magnitude system. I understand what these two magnitude systems are and how to convert between them.
My question is: what is the point of the two sets of filters being on different magnitude systems, one Vega and the other AB? It's not as if the Johnson-Cousins filter hardware physically has the Vega spectrum built into it, right...?
If I do aperture photometry on an I-band image and an i'-band image, will the first one return Vega magnitude of the object and the second return AB magnitude of the object, by default? And if I wanted to do SED fitting, then I need to be consistent such that all of my data points (even from other telescopes) need to be on the same magnitude system (e.g., convert the I-band Vega magnitude into an I-band AB magnitude)? (Or do that conversion first, and only then convert to flux units via $\nu F_{\nu}$ or $\lambda F_{\lambda}$).