The 'Malibu' cars like you said . . . have the 'Chevelle' emblem in the grill, they also have 'Crossed Flags' emblems on the fenders with an emblem for what size of motor was in the car '283' or '327' etc. There are 'Malibu' script emblems on the rear quarter panels, on the trunk lid should be a fairly large 'Chevelle' emblem that makes a slight V in the middle, and on the tail panel should be 'Tri-Color' emblem that is surrounded by chrome accent. This piece is fairly large, and hard to describe but if its on the car you'll know it . . . I hope it is . . . the Chrome is not currently reproduced . . . and they're getting harder to find in good shape. To my knowledge the only interior differences between the Malibu and 'SS' interiors was the Dash panel in front of the Passenger seat . . . and maybe the steering wheel . . . My 66 Malibu has a three spoke wheel with a 'Chevelle' horn button. I don't know the particulars on the steering wheels and what wheels interchanges with what models . . . but thats the wheel I have on my car and have no reason to believe its ever been changed.
Other then those cosmetic differences I don't know how you could identify a Malibu. I'm sure there are differences in things like springs, shocks, fuel lines, radiators, differentials etc. But I couldn't talk to these issues without feeding you a line.
There are currently a couple books in print that throughly document the both 'Malibu' and 'SS' restoration.
Just as quick as I get back from Iraq . . . I'm going to work on mine.
Best of luck