Hi
If you install Linux on a hard drive which is the only hdd in the system then the boot files will be on that hdd
Once the Linux installation is complete you will be able to re connect the windows hdd and use the bios boot menu to choose which hdd to boot from
By default windows can not see Unix file systems such as ext 2 ext 3 etc
Drivers are available to read and read / write Unix files systems from windows
Some free some chargeable
Modern Linux can read ntfs and fat 32 partitions and while in Linux you can decide which ntfs partitions can be accessed
Probably best not to mount the windows partition to ensure Linux can not change anything affecting windows
Depending on motherboard a F key goes to boot menu where you select...