One way to handle this is to put the information as an attribute on the primary one. I must stress, I really think this is the appropriate thing to do only when the two pieces of information are related such that one has information about the other.
For example, I sometimes stash the name of "crucial variables" or variables that have been significantly modified by storing a list of variable names as an attribute on the data frame:
attr(my.DF, 'Modified.Variables') <- DVs.For.Analysis$Names.of.Modified.Vars
return(my.DF)
This allows me to store a list of variable names with the data frame itself.