Welcome to Dell community, users to users base forum.  To better identify the issue, would you provide more specific information of the flexbay backplane you have.  Which flexbay did you use and the type of M.2 SSD, the type of drive carrier.  Pictures of connection setup will be great.

@Chino de Oro​

Hi! I'm using as a ssd a samsung 980 1tb nvme m.2, with a dell dpwc700 flexbay. As for flexbay backplane I don't know what model it is, but I'll leave a picture below (a picture with type of pins without opening the desktop, from the flexbay space). Also I'll leave some pictures of the wires connections. Thanks!

Your system backplane can support NVMe SSD in flexbay 0, which is the top bay.  If that was your boot drive on the top left, then the new Samsung SSD should be installed in the top right  I don't see any issue with your system hardware configurations.  You may want to check BIOS settings and verify that both of PCIE0 and PCIE1 are enabled (by default).

Hello, 

the pic you shown displays the nvme carrier having the correct green light, so the drive is recognized and considered ok, electrically ( the small green led under 512gb )

@mazzinia_​ 

@Chino de Oro​ 

Hi! I checked again bios and the ssd is showing, apparently I wasn't looking in the right place. So, as a context, I have 2 sata ssds one with windows on it and the other with ubuntu. Interestingly, on ubuntu the ssd is showing (not in files, on disks section), but on windows everything seem to be hidden (truly unidentifiable). I ll leave a picture of what is showing on ubuntu. Thanks!

As long as you can setup and access the new NVMe SSD for storage, not worry too much about the display info.  In RAID mode, the storage controller blocks some utility to read the drives properly.

@Chino de Oro​ Interestingly, I'm not in raid mode, just in ahci. I searched on google and some people say that the reason for not seeing the ssd can be due to ahci mode. 
1. Should I change to IDE mode?
2. If I change to IDE, does my system boot up normal?

on windows you need the drivers installed. Download the Intel RSTe drivers from the support page

My comment about storage behind RAID controller could not be seen by some utilities.  That was referring to the NVMe SSD connected through PCIe/SAS backplane.  This is the same issue when users could not see the intended boot drive during Windows installation.  My comment was not a response to your SATA boot drive.

If you are not able to access and format the new Samsung SSD to be used as storage, download and installing this driver.  It will help Windows with seeing the Samsung drive.

Not to be confused with your SATA boot mode, leave it at whichever the storage mode you installed Windows with.  Do not make change in BIOS settings, it may cause boot problem.  There is certain process for changing storage mode in BIOS without reinstalling Windows.  But that was not the issue here.

@Chino de Oro​ Now it works, thanks!