I have flashed the pre built demo packages of android into the kit.
But when I connect the kit with pc in device manager i get drivers missing for this device due to which i am unable to upload any application into it.

For Linux platform,there is no need of special driver for USB device.For Windows,please refer to Google USB driver page: http://developer.android.com/sdk/win-usb.html .Install the Google USB driver for Android,the you may use the tools to install packages.

i have installed google usb driver revision 4 but when i connect the kit and update the driver it shows that no drivers are found and contact the manufacturers.I even tried to send the .apk in sd card and then read it from the kit but no .apk were found in the kit.
Is there any other way to download application into at91sam9g45-evk? Can I use Sam-ba for that??

You still cannot install the driver? Here are the steps http://developer.android.com/sdk/oem-usb.html#InstallingDriver) .In fact we cannot install apk by sam-ba except you build the Android yourself and put your apks in.My suggestion is using Android adb tools. Our driver location: http://www.at91.com/android4sam/pub/Android4SAM/UsingAdb/usb_driver_atmel.rar

Thanks a lot.. kit is successfully connected with the laptop now..!! the only problem now is I cant shift the application to the sd card which limits the no of application being installed in the kit..