Did I do something wrong? Which coolant cap is which? HELP!

I have a mazda millenia '01: the engine ran hot the other day so after letting it cool I checked the fluids. Only problem, though major, was that my coolant reservoir was empty. I also opened the 2nd coolant cap by the engine that according to the manual is designed for refilling and flushing the coolant system: it was dry as well. SO I added antifreeze to the reservoir full line and added some to the other spot as well. I ran the car with the flush cap off for a minute or so to get the air out. I put a brown paper bag under the engine to check for leaks. A day and a half later: no leaks, reservoir is full, and the flush pipe appears overflowing. What do I do! Also I have heard that the 2 coolant caps appear identical but if placed on the wrong spot that that could lead to all my coolant escaping. Is that true? IF so which cap is which?