Hello Sergi!
Please ensure that on the General tab of the product settings page in “Post types used by WRI” field Products and Portfolio checkboxes are checked (I suppose they are custom post types).
Please also ensure in “Screen Options” on Product and Portfolio edit pages (upper right corner) that “WRI Manual Relationships” checkbox is set.
If the two settings above is done, then “WRI Manual Relationships” metabox have to be displayed on Products and Portfolio edit pages, unless the 3rd party plugins that create these custom post types do not remove it.
Regards,
Peter Rath
WebshopLogic