You can request IFR clearances from any ATC at any moment.
You’ll need to enter your flight plan in the plane’s navigator. You’ll have to learn to use the cockpit instruments (g1000 g3000, g3x, etc…) In order to set up the flight plan in mid air.
(departure airfield, destination airfield, are mandatory. Waypoints, SID and STARs are optionnal).
Once the plan is set in the plane’s navigator, the ATC window will have a new option appear in order to ask for IFR clearance.
Note that you must use an airport as departure and destination fields (setting a departure with a waypoint will produce bugs when trying to set up the approach).
If you wish to modify the destination, the way to do it in the SIM is to just modify the route in the navigator. Then the option to ask for a new IFR clearance according to the new route will appear again.
For the departure airfield, you do not need to perform a touch and go at the departure airport. You can just choose any airport near you and the game ATC will direct you to the nearest waypoint from your current position (just like activating IFR when taking off from uncontrolled airfields in real life)
(The same thing will happen if you change a did/star/approach)
For altitude however, the ATC will automatically calculate a default cruise level. If you want to change it, you’ll ask the ATC for a level change later