1. What is the best method of a dual boot system Windows and macOS (I have read a number of methods)
Install Windows as normal (usually best to remove your intended macOS drive before installation) and then put your second drive back and install macOS. You can use Clover to boot your Windows partition. I usually set a timeout of 10 seconds so that I can easily select between both.
2. How do you control the bios for dual boot, I am going to assume the BIOS for windows and macOS are not the same ?
Settings used for both are the same. Unless you really need Vt-d (likely not), the BIOS/UEFI settings will work on both if you're using the settings as per the initial guide.
Whats the best storage file format so that both macOS and Windows can read and write from it.
In my opinion, I would go with NTFS and then just install a NTFS driver from Paragon Software or an alternative in macOS.
If you want, you can do it the other way around by installing an HFS+ driver in Windows and using the native HFS+ format in macOS. I wouldn't do APFS since your only option would be the Paragon Software plugin in Windows and it's also less mature than equivalent HFS+ drivers.
My reasoning behind formatting it as NTFS is that generally you would consider your Windows installation to be more 'stable' than your Hackintosh installation and IMO it's important to have access to tools like chkdsk and such in the native OS as needed. In my opinion, HFS+ doesn't feel as robust as NTFS. Linus Torvalds (creator of the Linux kernel) has even gone as far as saying (he's somewhat…opinionated) that it's the worst filesystem still in use today.
Some people will say you can use ExFAT, but it's not a journalling file system so it's more prone to data corruption in the event of a crash or power outage. It also tends to be not be very space efficient.