Hi Alex,
stack.xml can only be produced from Solution Manager, but you still can proceed with patching individual components (for example, applying patches / code corrections provided via SAP Notes) even if you don't have stack.xml and due to any reason cannot generate it. As an alternative to option involving submitting generated stack.xml, you can use an option "Manually prepared directory" and specify location of the archive files that you downloaded and that contain patches which you want to deploy. Refer to SAP Note 1641062 and Manually prepared download directory option from Software update manager (SUM) tool - Software Logistics - SCN Wiki for more details.
Regards,
Vadim