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In my azure virtual machine i selected windows server 2008 r2 image from quick created. When I log into the machine, i see there are two drive. On which drive i should ftp my application because I am not sure which drive will persist if machine is moved.
Also how much data i can persist on each different type of VM, is there a limit depend on my vm size?
In Windows Azure Virtual Machine for Windows you can find drive C and D.
Drive C is the boot OS disk and the size is actually the size of your VHD you have either uploaded or configured from the Gallery. This disk is the persisted disk so anything you will store on drive C will be persisted. In the preview the Windows Server R2 VHD from Gallery id default 30 GB in size that’s why you may see 30 GB size in drive C: however you can create upto 128 GB VHD and deploy by your own with medium and above Virtual Machine instance.
The storage space on drive D: is the temporary storage as indicated in the above table, where a Medium is expected to be 100 GB. This space is NOT peristed in Windows Azure storage and will be destroyed if the Virtual Machine needs to be migrated due to bad hardware.
About your question on how much data can be persisted on Windows Azure Virtual machine, the data size which can persist on Windows Azure Virtual Machine is documented here.