CartoMobile uses shapefiles as its native format, so you will need to put your data into shapefile format in order to open them in CartoMobile. Once you have the files, you may drag them to the CartoMobile file window as described in the documentation.
If your Cartographica mapset uses referenced files, you can just drag the .shp,.shx,.dbf, and .prj files into iTunes as described in the documentation for CartoMobile.
If the data is stored inside of the MapSet, then you will need to export the layer. To do this, select the layer and choose File > Export Layer... and you will be prompted for the location to store the exported files. From there, you can just drag the .shp,.shx,.dbf, and .prj files into iTunes as described in the documentation for CartoMobile.
Versions of CartoMobile prior to 1.0 required that all data be in WGS84 Lat/Long format. We strongly encourage users of CartoMobile to upgrade to 1.1 or better of CartoMobile.
Note: It is essential that all shapefiles imported into CartoMobile have at least one data field. Current Cartographica versions are capable of creating shapefiles with no data fields (these generate no .dbf files when exported). If you cannot find the .dbf file, use Window > Show Layer Info to add a field to the layer before exporting.