GDPR is looking at personal data on a legal company level. Consequently you need to make your analysis on a legal company basis. if you are sharing personal data between group companies this needs to be handled under the appropriate rules for data transfer/data processing with GDPR.
Currently ComplyTo only supports one company in the analysis (but we are working to include a corporation/group company functionality in the future). You can document your subsidiaries in step 1 of the wizard, but strictly per GDPR you need to perform specific GDPR documents and analysis for these separately.
Currently the only option in ComplyTo is to create one account per legal entity.