If your project has a single data-collection effort, and if the 3 projects do not depend on one another (ie they could be conducted in parallel and they are not sequential), then a single preregistration might be best, as long as you note in that preregistration that the results will be reported separately (you want to avoid the impression that the first paper coming out is only reporting a biased subset of the analyses- if you prespecify how results are reported then it is a clear justification for this "selective reporting" which is problematic only if it is informed by unexpected trends in the dataset).

If your data collection efforts will be distinct or separate from one another (either in time or in methodology and organization), then multiple preregistrations will likely make the most sense.

If the studies include exploratory that work is designed to inform latter confirmatory studies, then definitely wait to preregister until the exploratory work is completed. Make sure not to analyze any specific data as part of the exploratory stage that will also be used for the confirmatory work. If your design requires that a single data collection effort be used for both exploration and confirmation studies, then you can randomly hold out a portion of the data and use part of it for exploration before opening up the reserved portion for confirmation (see "Hold out data-sets or split samples" above).