A V3 Substance is more like a V2 Molecule. The V2 Molecular System is probably most closely related to a V3 Sample (which in turn contains Sample Components that are Substances). When you add a sequence / Chain to V3, it automatically creates a Substance at the same time. So that will happen both for your protein and your peptide.
You can then also create small molecule Substances, e.g. DMSO and the one you are titrating in.
You can then create as many Samples as you wish, e.g. apoProtein, ProteinWithPeptide, ProteinWithDMSO, ProteinWithSmallMoleculeAndDMSO. You can then in turn link each of your spectra to the relevant sample (go to Spectrum Properties by double-clicking on the Spectrum in the sidebar and select the sample from the drop-down in the General tab).
I suspect, however, that most of this is actually optional. By all means do it for your own book keeping, but I don’t think the program will really do much with this information.
The Chemical Shift Mapping module will basically do most of its work based on a SpectrumGroup. So in your case you probably want to create three SpectrumGroups. One for the peptide titration, one for the DMSO titration and one for the small molecule+DMSO titration. In each case, place all the relevant spectra (plus always the apo protein spectrum) into the Spectrum Group (either double-click New SpectrumGroup in the sidebar and then move the relevant spectra into the Included box by dragging or double-clicking; or select the spectra in the sidebar that you want to include, right-click and select Make SpectrumGroup from selected).
In the Series tab of the SpectrumGroup pop-up you can then enter a variable that changes over the series. This is the like the Series pop-up in V2 and in your could would probably be the peptide/small molecule/DMSO concentration.
As for telling the program that there is a DMSO control: I don’t think that is strictly possible at the moment. Is this something you were able to do in V2 (I wasn’t aware)? Did you specify a second series in order to correct your chemical shift changes? Or was there a specific equation you used? If so, it would be great to know about this.