Its fine now, I solved it last week and thought I could share the solution as it is no where to be found on the web.
Step-by-step configuration guidelines to use GeoJSON file in GeoAnalytics:
In the ID tab : put the dimension name that matches the JSON key attribute, does not need to be the same name but must have common values.
In the Location ID Tab : do not put anything.
In the layer option : just select the correct map id, you can modify the other fields as you wish.
In the location options tab :
-Location source = dimension
- Service URL : Geoanalytics requires your json file to be stored under https as it does not support cross-domain security.
-Select GeoJSON file in location service Type
-Source key attribute : the key attribute values of the JSON must match the dimension field values. Lets say your dimension is called my_dim with values in [0,1,2,3,4,5,6], your JSON key attribute can be called my_dimension but have overlapping values (ex: [2,3,4,5,6])
-Configure the rest of the tab as you see fits
In the aspect tab :
under colors : put colors to custom, select measure in the drop down (if you want to color using a measure) then select the measure you want to use. Select your chromatic chart and you are done.
The same guidelines can be used for any type of layers.