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Not 100 percent sure what you're asking. You use Alt-drag to replace a layer's footage source with another footage item. You can't select multiple layers and then Alt-drag multiple new sources in one step - you need to do them one by one.
Yepp, exactly as Andrew said - one step at a time. How else should AE know which footage you wanted to replace with the other?
How do I replace a layer with different footage from my sources folder and still keep all of the properties?
select item in timeline to replace.
select item in project window to replace it with.
hold alt and drag project item onto layer in timeline.