If I understand correctly the second part of your message, you can input 3 images for e.g. :
Then in the module NamesAndTypes >> use "Images matching rules" >> select "Files__Does__Contains__", >> "channel_1" named as "Red", "channel_2" named as "Green" etc...
Alternatively, you can use module Metadata and capture the number comes after "channel_" as a metadata "channels", subsequently in NamesAndTypes >> "Images matching rules" >> "Metadata__Does__Have ChannelNumber matching__"
Hope you get the ideas?
It's not so convenient doing the first way, i.e. first merge images by ImageJ and use CellProfiler to split them back again.