Hey I've been extensively using linux distros on VirtualBox and am looking to install / make the switch to a dedicated native install on a SSD in my desktop. Currently I have Windows 10 with allot of config/programs/data spread across 3 drives, this SSD will be the 4th. I'm planning to disconnect the drives and install Manjaro and Ubuntu side by side on the SSD. I'm planning to then reconnect all drives and choose the boot HD from the bios menu, and then choose Manjaro/Ubuntu via Grub if the linux SSD is chosen. Here's my concern/question. Can this cause issues with Windows drive lettering and detection (I vaguely remember having this issue many years back, which wrecked havock on pathing)? Any other major problems this could cause, I have allot of work on my Windows machine I don't want to hose, but equally want to run linux native rather then through virtualization for a number of development reasons.

Sounds ok - in my experience Windoze only assigns drive letters to filesystems it recognises. Your Linux filesystems will be unknown. Never had a problem like that - Linux yes, Win no.
Once you boot up Linux update your grub config and boot Windoze from there - saves having to mess with the BIOS.

I used the BIOS way for a week or two. Much easer to do it with updated grub as sygOO suggested. I first started opening the case and switching the cable to the drive I wanted to boot to (wow, did I do that?) Then went to the BIOS way. After using grub it was way better.

Chris.

Interesting, looks like you went through a similar setup (and thought process, yes I considered switching cables). I'm avoiding grub being aware of my Windows install on purpose to avoid any possibility of it messing with the windows boot process. Happy to use the BIOS if there are no technical (other then for easy of use) reasons not to, ongoing. On SygOO comment, your probably correct, in fact the drive lettering issue I mentioned may very well have been 2 different windows installs causing conflicts, not Linux.

Thanks for all the answers, I think I have the confidence to make the leap now.

You'll be ok if you remove the Win drives while installing Linux/grub. Grub will chainload Windoze without impacting it.
Problems (for Windoze) arise if you leave the drives connected and grub replaces the Win loader in the MBR. Normal Win updates are ok with it, but Service Packs and new versions (Win10) moan if they can't find the Win loader. In your case you would just need to switch the BIOS boot drive back to Win if the update whinges.

Windows 10 and no mention of UEFI? If you are using EFI this can create additional problems. If not EFI, it should be simpler and the suggestions above should work with no problem. With regard to drive lettering, my experience is that it is not possible to give a drive letter to a non-windows (or at least to a Linux filesystem) partition. The best you can expect is to see 'Healthy partition" in Disk Management.

What a helpful community, thanks to all the responses. I checked my C:\Windows\Panther\setupact.log and found I am not running UEFI
Callback_BootEnvironmentDetect: Detected boot environment: BIOS

This should mean I am not, so the above directions should work without problems I understand. Thank you.

Windows knows nothing about ext4 partitions, so this partition invisible for Windows and Linux installation will not change partitions order and lettering i.e. how they appears in Windows. There shouldn't be any problem with accessing your old data from Windows.

You can detach your drives while installing Linux. It would be very useful if you had different Windows with different bootloaders: e.g. Windows 7/8/10 and Windows XP. Since you have only Win 10 installed, no matter will you detach your drives or not.

If you have some extra bucks just buy an external USB Hard drive or Thumbdrive install Linux distro of your choice and boot via USB.

In this way you don't have to mess up with the internal drive of the laptop.