Well I have had mixed results:
The first three examples here use a VM of a Linux distro to create and modify clones of USB and VDI disks and partitions:
It is possible to create a VDI clone of the iso disk, but the file system is read only
It is possible to "dd if=... of=..." a bootable clone of the iso CD at the front of a larger VDI and then add further partitions and even get the 'cloned' iso on VDI to install to the rest of the VDI, but unlike the next example, the cloned OS partition will only boot to itself and refuses to accept the just created 2-4th partitions as writable so it will not save Resident info therein.
Another direction is to install old RemixOS to a USB stick and let the VM open the USB port to a Linux VM and "dd if=... of=..." copy the USB stick to a VDI file but I have found that that VDI will not boot even if you set the boot flags. Interestingly, if the second partition (REMIXOSSYS) on the VDI does not mount automatically, you can boot to the iso CD on any of the Sata ports 1-29, and the VDI you 'cloned' on Sata port 0, and when you select Resident mode booting the CD, the CD sometimes finds that second partition and inserts a compressed data.img file on that partition (4GB only) which it then mounts in RAM and it becomes your resident "drive". I do not favour this method as 1) there is only 4GB available for resident data and, 2) the rest of the disk image is inaccessible. There is one more thing about this set up, if you run "Update OS" from within the RemixOS program, more compressed image and SquashedImage files (about 6GB) will be added to the REMIXOSSYS partition on the clone of the USB. When you reboot this combination, the iso CD starts the boot process and the VDI HD finishes from this mounted files that were added. So you are running in a form of resident mode.
Success! Here is a screen snap of the VM running on my iMac.

So I elected the simplest method and it works well and you can even tweek the result so it is always in Resident Mode (using a Linux VM).
I use a iMac (El Capitan) and run VirtualBox 5.1.6 r110634 (Qt 5.5.1), so the literal commands may be slightly different for you
- I used the latest Remix_OS [Marshmallow_v6.0]_v3.0.207_for_PC_Android_M_64bit_B2016112101 installer on a Windows PC and install to a real 16GB USB stick.
- I mounted the USB stick on my host (iMac) -- note the VBox program is NOT running at this time
- From a command/terminal window having full 'root' privileges, I run the VBox command "VBoxManage convertfromraw source destination" to create a VDI clone of the USB including all the partitions (3: two VFAT and one EXT4) , file systems and boot sector flags
root@aarc01:/Volumes/Data/vbox/VDIs/# VBoxManage convertfromraw /dev/disk2 remixos.vdi
On a Mac one has to have root privileges to access the device root (in this case /dev/disk2 directly) as even the owner user can only access the partitions on that device (ex. "/dev/disk2s2" a.k.s the REMIXOSSYS partition). Depending your Linux set up and user permissions, you most often also need 'root' privileges to access the USB device's complete file system.
4. I remember to make my usual VBox user that VDI file's owner.
5. I now just attach that VDI on a SATA controller Port 0 (no other attached devices) in my VM:
- no EFI,
- 4 CPUs,
- 3200 MB ram,
- 3D acceleration,
- Scale Factor 140% (to vertically fit my 1920x1080 monitor),
- PIIX3 motherboard,
- PAE/NX & Nest Paging, and
- the PCnet-FAST NAT adapter.
Fire it up (don't forget to disable mouse integration) and maximize the screen, finish the install of the RemixOS options and enable Google Play and you are good to go
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If you do not know how to get root privileges in Mac or most Debian distros, there is a back way in--the sudo command to launch a root shell-- "sudo -s" in a terminal. You will then be root (master control). Then use the command "passwd" to set a password for root. Then you may exit the terminal and at any later time, you may from any terminal just enter "su" and root's password and you have master control of the computer. If you can not access the sudo command there other work arounds but this is not enough room here to go into that. ArchLinux and SUSE type distros can't do this, but you can set the 'root' password at installation.
If anyone wants to host a zipped copy (1.61 GB) of the basic ready-to-go RemixOS v3.0.206 with Android v6.0.1 VDI on their cloud space and make it available to this thread, let me know and give me a link to upload that file to that space.