I have multiple binary rasters (calculated from raster calculator) in ArcMap. Now, I want to convert them all into one raster. Mosaic and Composite tools of ArcMap seem not helping here. I am not sure how to proceed with this. Eventually I want that 1 output raster as an input in MaxEnt.
It sounds like you have multiple neighboring (and in slightly overlapping) rasters that you would like to merge into one larger raster. Based on the comments, perhaps habitat for a migratory species?
I would suggest Mosaic to New Raster as that won't involve overwriting any of your existing rasters, and will let you choose how to deal with overlap (max, min, etc.).