ER 3 states:
The devices must achieve the performances intended by the manufacturer
and be designed, manufactured and packaged in such a way
that they are suitable for one or more of the functions referred to in
Article 1 (2) (a), as specified by the manufacturer.
Your packaging must therefore be sufficient to protect the device and you must be able to demonstrate that you meet this requirement. How you do that is up to you.
If you can demonstrate that your device is ok being wrapped in tissue paper then that is fine. If you decide that it needs to be packaged in a metal crate with integral suspension then that is fine too - it is really up to you!
With regards to how to demonstrate that it is capable, there are 3 methods I can think of off the top of my head:
1. the easiest (but least thorough) is taking using the packaging solution for another product that has similar concerns during transportation/storage.
2. If that isn't possible you could do a variety of tests, depending on what your risk assessment has identified as a possible cause of failure - drop test, vibration test, thermal/humidity test, pressure test etc.
3. Package up your device and send it out with your standard couriers to your most obscure location, then get it sent back
With regards to whether you should work closely with your packaging supplier or get someone to design it for you...I can't answer that, all I can say is that it is important that it is done right!