Most tournaments use ratings to determine the pairing numbers. However, particularly in team tournaments, it is not uncommon to use seedings based upon "regular season" results.
The best way to put in the seedings is to use the "local rating" field and tell WinTD to assign pairing numbers based upon the local ratings (see Add/Edit a Section). To have this work correctly for a team tournament, you need to check the Use Input Team Ratings in the Team Tournaments tab in the Preferences Dialog, as otherwise WinTD will compute team ratings based upon the average rating of the team members.
The one thing to remember, of course, is that seedings are usually set with the top team as number one, with teams becoming weaker as the seeds increase. Ratings, on the other hand, work from top down. You can work out a reversed mapping (#1 seed = 100, #2 = 99, ...), but you might find it simpler to use -1, -2, -3,... This gets everyone in the right order and it's probably easier to tell people to ignore the - sign than to explain what "100" means.
The one big problem that you face in using seedings rather than ratings is that the color allocation rules need adjustment. The standard alternation and interchange limits of 80 and 200 are meaningless when the "rating" fields don't have ratings in them. You should set the limits based upon how many seeding positions you are willing to allow in a swap to correct colors. An alternative is to use the None (FIDE style) box for the rating limits, but then to check the "Avoid Interchanges" box in the Preferences Dialog. This will let WinTD do any transposition, but no interchange.
You don't necessarily have to seed the entire tournament. You can, for instance, have a group of top seeds, another of second seeds and lump everyone else together as unseeded. Assign a "rating" of -1 to the top seeds, -2 to the second seeds and leave all the others "unrated." WinTD will then randomly shuffle the -1's, -2's and unrateds each time it pairs a round.
WinTD Help Contents
Team Windows
Team Files
How To: Add Players to a Team
How To: Add Teams to a Team Section
How To: Change Board Orders of a Team
How To: Create a Team Tournament Section
How To: Enter Scores in Team Sections
How To: List Individuals in a Team Section
How To: Show/Print Team Standings (combined tournaments)
How To: Show/Print Team Standings (team tournament)
How To: Use Master Files for Team Tournaments
Team Tournaments
Dialog Box: Add/Edit a Section
Dialog Box: Add/Edit a Team
Dialog Box: Board Results
Dialog Box: Board Weights
Dialog Box: Team Scoresheets
Dialog Box: Team Setup
Samples: Team Pairing Sheets
Samples: Team Standings