Atlas now has some tooling that is 24 years old... so there are a bunch of different generations and as to what line they currently fall in... that depends.
The old Roco line is no longer part of Atlas. This would be the 1974-75 SD24, SD35, GP38, GP40, and FP7.
The Kato line - RS3, RSD4/5, RS11, RSD12, RS1, C424, C425, and GP7 - are now part of the "Classic" line although I don't think the RSD12 has been re-issued because it's a kludge.
The later Roco stuff - S2 and S4 - are now part of the Classic line.
The Classic line stuff is made in China, no longer by Kato/Roco although the shell tooling is the original, upgraded somewhat.
The "Red Box" line introduced in the early 1990s consists of the U33C/U36C, C30-7, U23B, early GP40, and AEM-7. These are roughly equivalent to current Silver series and I think the U23B has been re-issued as a Silver.
The "Master" line began with the GP38. The GP40 was moved up into the Master line on later runs. Master series came with the switchable dual mode DCC decoder.
At some point after that (2003?) Atlas introduced the Silver Series, which are the same as Master series but without the decoder - instead having an 9-pin NMRA socket. Essentially the same as the Red Box, but the lines have not been completely merged yet from what I can see.
The Gold series comes in larger boxes and they are equipped with QSI sound. The Gold has technically replaced the Master series - if you want the factory DCC, you have to take the factory sound with it - however, there have been some additional runs of previous Master series locos since the Gold series began.
The Trainman line is a brand new line that has a simplified shell and fewer details but retains the same drive components and design as the higher end stuff. Internally they are the same as Silver, I believe - no decoders but 8-pin plugs.
For future production it looks like Atlas is wanting to stick to three lines: Gold, Silver, and Trainman. The Classic line will likely be continued also, since there's no other place to put it. The Red Box and Master line appear to be dead at least for new products.
The newest releases - Train Master, C420, GP40-2, etc - have been available only in Gold or Silver.
Andy