Seating Management: What makes your suggestion (seating players immediately upon buy-in) difficult for the TD is that you probably know how many players will be playing, but at that point in time, the software does not. Therefore, how can it know how far out amongst the tables you have defined it can spread those players? The seating algorithm is always attempting to
minimize the seating - moving players as close together as possible to eliminate unnecessary seats and tables. This also hits the situation where you have 9 players but want to seat them at 2 tables (of 10 seats each). This just makes no sense to the seating algorithm.
Here's how you work around all of this: Buy all of your players in before-hand, but do not mark them as "Paid in full". Once they are bought-in, you can seat them. As players actually arrive and pay, you can mark them "Paid in full". Once you are ready to start the tournament, remove those who are not "Paid in full" (the Undo Buy-ins and Remove Players dialogs both have shortcuts which will select only those players who are NOT "Paid in full").
As for seating 9 players at two tables, you can either do it yourself (drag and drop players), or reduce the number of seats at those tables. Double-click the table name and changing the number of seats. Quick and easy.
Add-ons before the tournament starts: I'll add this to the to-do list.
Scrolling screens:
http://www.thetournamentdirector.net/faq.html#faq21Payouts not right: rounding to the nearest will always literally round to the nearest. If this causes the payout to be too large (bigger than the actual pot), you'll probably want to round down. Then set which of your prizes will get whatever is leftover (share leftover pot).
Here's an example: Pot is $150, prizes are 1st place 70% and 2nd place 30%. This works out to 1st place $105 and 2nd place $45. If I want to round to the nearest $10, rounding takes the amounts to $110 and $50, for a total of $160. Exactly as you described. How do you resolve this? Probably one should be rounded up while the other is rounded down. But which one? Both prizes are technically equally eligible to be rounded up. Different people will have different opinions of this. So this is where the software says "I've done what I can, you have to make the final call".
You can round them down and set one of them (probably 1st place) to be the recipient of whatever is leftover. Which would make the prizes $110 and $40. Or you can simply override the amounts to be whatever you decide they should be.
History: On the Players tab, double-click a player. From there you can edit the player's history (edit the buy-in, any add-ons, rebuys, and bust-outs, and undo some of them). Up-coming version 2.2 will allow you to do much more, including inserting add-ons, rebuys, and bust-outs into a player's history.
Every aspect of a tournament can be saved individually in template files. You can also set a saved tournament file to be your "default" tournament. On the Preferences tab, press the Config Files button.