Best advise I can give you for using TD3 for larger events is only use the player movement suggestions for the initial seating draw, as per TDA RROP rules etc, you will be balancing by taking your Big Blind from tables, using the software to electronically track players movements is time consuming and cumbersome.
Once I have the registration done, and the seating chart is no longer required the names on the system no longer matter to me, so I just use the "bust any player" method to keep the plasma display player count/average chip count correct, everything from there on in is manual, and you can put the correct names back in later on when you get close to the money. I have did a 180 player event where we tracked every movement, but that had a Gaming Inspector operating the PC whilst a Floor Supervisor or TD did the balancing, radioing through the movements to be kept up to date, that takes quite a few staff, whereas doing it manually requires only one person to run the floor, even when there is 200-300 people participating, which I have done a fair few of in my time, I do also have a very good system where I use laminated seat cards with the table and seat number on them, the cards get handed in when a player busts, and then I simply keep them in front of the computer and they tell me what needs balanced, what needs collapsed and how many players are still in.
If you are doing late reg like Jody says, open 7/8 handed and when you get a queue of 7 or more put the whole lot straight onto a new table. The hardest part of running any tournament is getting everyone registered and sat down, the rest is simple enough providing you don't attempt to over complicate it.
EDIT: One thing I did just consider is that perhaps you meant you usually have the tables set up on the software before registration. It's faster and easier to use the add tables feature to create the amount of tables you require with the amount of seats you require once you have done registration, Auto Seating players during registration for an open event is pretty nonsensical in my eyes, and it only takes an extra few minutes to get every one seated, by generating a random draw after registration has closed, which get's everyone seated from the number 1 seat on each table - for example if you have 60 entries with late reg to come, click add tables, number of entries 60 seats per table 7 number of tables required 9, gives you 9 tables, 6 with 7 players and 3 with 6 players, and your number 8-10 seats will be empty on tables 1-6 and your no 7-10 seats will be empty on tables 7-9, leaving you 30 spare seats to manually fill during late reg.
Regards
Stuart