If I understand this correctly, the only way to really do this is to create a custom prize level configuration and use the Automatic Prizes feature to implement it. A little bit of a pain, but it's a one-time effort.
What you would do is define what the prizes would be for each "level" of players. Meaning, if you had, say 7 or less players, you will award one $50 prize to 1st place. For 8-12 players, you award $50 prizes to 1st and 2nd places. Define these levels all the way up to the largest tournament you expect to have, place this all into a configuration file, and then let the TD do the rest.
While you cannot create a prize that awards both a fixed amount ($50) plus a percentage of the pot (10%), you CAN award two prizes to the same rank. So, taking the example of 8-12 players, you would create prizes:
1st, fixed, $50
2nd, fixed, $50
1st, percentage, 50%
2nd, percentage, 50%
Fixed-amount prizes are removed from the pot first, then the percentage based prizes are calculated from the remaining pot. (This is always the way they are calculated - not just because I listed the fixed-amount prizes first above; just want to avoid any confusion around that.)
For 43 players (your example): create fixed-amount prizes of $50 for 1st through 8th places. Then create percentage-amount prizes for places 1st through 8th with percentages of 100 / 8 = 12.5%.
You'll do this for each "level" of players and enter this into a prize configuration file. Set the software to use your custom prize configuration file for the Automatic Prizes feature, then turn on Automatic Prizes when you run your tournament. As players buy-in to the tournament, the prizes will automatically change to reflect the proper payouts.
This all sounds a bit complicated, and it is, but again you'll just need to do this once and you'll be set. Take a look at the user manual, in the Prizes section, and read about the Automatic Prizes configuration. I believe this is section 11.8 in the current user manual (version 2.5.3). That should get you started. If you get stuck, feel free to continue this thread or email me and I'll be happy to help.
To get you started:
<prizeLevel minPlayers="1" maxPlayers="7">
<prize rank="1" name="1st Place" percent="100" />
</prizeLevel>
<prizeLevel minPlayers="8" maxPlayers="12">
<prize rank="1" name="{1} Place" fixed="50" shareLeftover="true" />
<prize rank="2" name="{1} Place" fixed="50" />
<prize rank="1" name="{1} Place" percent="50" shareLeftover="true" />
<prize rank="2" name="{1} Place" percent="50" />
</prizeLevel>
Ugh, I just tried this and it appears it won't work. The theory is sound, but the configuration file verification is a little over-zealous. That means that it WILL work, but you have to manually configure it. When the TD loads the configuration file, it sees that you've awarded two prizes for 1st place (and for 2nd place), and assumes you have made a mistake. This should be a warning at most, and should not prevent using the configuration file. I will fix this for the next release. Sorry!
For the scanner/barcode use: do a search for this in the forums, it has been discussed before. The short version is to turn on the "Allow Find on player dialogs" preference (on the Preferences tab, Miscellaneous section). This should enable the Find feature on every dialog in which players are selected, including rebuy and add-on dialogs. The software obviously won't "automatically" detect anything as an add-on or rebuy. You'll have to initiate the add-on or rebuy dialog and then scan the card and continue through the dialog.
Sorry for the delay in responding. The first little Cooper was born and my support time has been compromised! I may be a little slower in responding over the next few weeks, but I will do everything I can to continue to support the software to the best of my ability.