Hi Simone,
It is possible to use your own gas column density distributions as long as it follows the format required for GALPROP. It does not allow for much freedom.
The maps should be in CAR projection with the galactic center at the left boundary of the map and l increasing to the right. This is opposite to the usual convention.
The maps should be split up into galacto-centric annuli with the annuli boundaries given in a table in the first extension. The CO and HI maps should have identical boundaries.
It should be best to try to imitate the files distributed as closely as possible. There is very minimal error checking when reading in the files so you should carefully check the results.
For a description of how we generate the annuli maps for GALPROP, please see the appendix of
http://adsabs.harvard.edu/abs/2012ApJ...750....3A