Hi Marcelo,
As far I remember, it should be possible to assign set types to category belonging to 2 different hierarchy. Unfortunately, I do not have access to CRM box to confirm the same.
Regarding the second question, it is better to make sure customizing setting identical between CRM and ECC. In most of the scenarios, ECC is the leading system and download to CRM/fixing incorrect/missing data is easier. Thanks to CRM MW.
Its better to upload few product from CRM to ECC, using 'Send to ERP' button and observe how category/hierarchy mapping happens to Material Type/Product Hierarchy in ECC.
Also, there should be customizing in CRM, to automatically upload the product created/changed in CRM without the need to press 'Send to ERP' button every time. But I am afraid , there is no provision of mass upload feature unlike Initial Download from ECC to CRM.
Hope this helps.
Best Regards,
Shanthala.