Syncing App Question iPhone

I tried to find an answer to my specific situation but I did not find any answers that I thought fit my situation. Here is my situation...
1) I have NEVER synced apps with my iPhone & iTunes. I would like to start having my apps synced. When I check the box in itunes it pops up a window telling me that the apps will be replaced with the apps on this computer.
2) I have right clicked on the iPhone in iTunes and used the Transfer Purchases. So all of my apps show up in iTunes.
3) If I now do the sync will my applications that have data saved in them be restored with the same data in them? I have a gas mileage app. I do not want to loose the mileage data that the app stores.
Thanks in advance for the help.
MacBook Air(2010) 1.86 Ghz & MacBook White 2Ghz & PowerMac G5 dual 2.0GHZ PPC Mac OS X (10.6.5)