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I have my own scripts and program that I need to be running on the X11.

I have: mkdir /usr/mystuff
And put my stuff there and then added cron jobs that start my program.

But when I do an firmware upgrade everything get wiped only the cronjobs for the root user will still be there.

My question:  How can I make sure my own stuff will still work after a firmware update ?

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Option A: Place your custom script it "/etc/config" directory. Its contents is untouched if firmware upgrade is done with "Keep setting" checkbox selected.

Option B: Place your custom script in any directory you like. Than open "/etc/config/sysupgrade.conf" file and enter path to script's directory. Directories, which will be listed in this file, will remain after firmware upgrade with "Keep settings" checkbox selected.

Is it also valid for the RUT955 ?

Yes, this is true for all Teltonika networking devices, at least if your device is running not very old firmware version (older firmware versions might not have "/etc/config/sysupgrade.conf" file)