That has nothing to do with you being jailbroken, it's an iTunes policy issue. The problem is that iTunes regards one app downloaded from two different stores (in your case US and Czech) as two separate apps.
I would advise you to do the following thing: log into iTunes on your desktop with your Czech account and sync the phone. That should log you into the iPhone iTunes app as well. Just to be on the safe side, go to your Setting app -> App Store. There you should be able to see your Czech account (if you, tap Sign Out and enter your Czech account).
Once you are logged with your Czech account in both the iPhone and iTunes, the simplest approach is to upgrade the apps as updates become available. Note, however, that paid US apps will have to be purchased again; with free apps there are no problems. You should check whether an app is free/premium prior to upgrading (simply search for it in the App Store). Also when upgrading a free app, iTunes will ask you if you want to "buy" the app. Don't worry about the word "buy", you won't pay anything.
And lastly, you should know that there are apps (like Pandora) which will simply not work outside the US.