In Ubuntu, you may need to mount the Windows partition if this doesn't happen in the bootloader, probably grub. Ubuntu should have no trouble working with NTFS.
As for the password issue, that's probably because you installed them as root. This is quite common, but you will then be prompted to supply your password. Is it also asking you to start them with sudo?
As for booting Windows by default, you may be able to do that from within the machine's BIOS, or by editing the boot.ini file on thee C: partition.
For the future, when it comes to rebuilding the machine, I strongly advise you not to partition its hard disk. Pick the OS which you use most often and install that. Then, download and install VMWare Player and run the other OS as a virtual machine.