Last first: How can I understand categories better? Practice :) and study:
http://support.tixati.com/categories
There are 2 types of categories, Status and Normal. There are 8 pre-defined Status categories which can be seen when you open the ADD Category dialog and select (x) Status.
Normal categories are simply labels you create to organize your torrents and Tixati allows assigning several settings to each specific category, i.e. a different folder to store when done. Again, see and explore the Add Category (x) Normal dialog.
Now onward...
You didn't indicate how many torrents you are dealing with but Tixati does have absolute limits for UL and DL slots, with an option to 'recycle' unused slots between these 2 so you could Seed up to 2000 total (if your resources can handle it).
To move torrents out of the queue or standby, all you need do is turn off the new and amazing "Auto-manage slots" function and then open more slots by manual setting.
There are issues still with 'mega-seeding' which are actively being worked out, after you sort out your torrents in Win 7 and you have several hundred torrents you want to seed, you might well re-enable 'Auto-manage slots' for UPloads. Then set Upload slots to 10-50 or so, experiment here. This will rotate through all your seeds, testing for existing demand and if none, those torrents get sent to standby until auto-tested again later.
http://support.tixati.com/transfer%20queue%20management