As the IFR capabilities are quite new, I fell free to tell some of my experiences in handling IFR flights.
Maybe i am doing something wrong and there is a‌ already a good way of handling some Problems which I do not know.

in general, I do the routing and filing my flight plans with autorouter.aero which works perfect.
Via telegram, I get a SD-flightplan-file, which I can directly open on my iPad - works flawlessly.

Case 1:
EDFZ->EDDV, IFR
The Routing loaded, SD has about 5 Waypoints in this case, ending on EDDV.
As usual fro German ATC, my flightplan is just rubbish 15 miuntes after departure.
I get a direct-to ‌‌‌‌‌‌‌‌‌a waypoint which is NOT on my filed route, but nearby.
- Therefore, I set a direct-To on SD in flight.
- ‌F***!!!!‌ My complete Routing is lost, i have a new one ending at the direct-to, but not at EDDV
- As a consequence, I add EDDV again after the direct-to
- Later on, i can load the Approcah Chart and fly it - great!

Case 2:
EDDV - > EDFZ, again IFR  with departure-route this time
the generated flightplan contains already the departure-route with waypoints.
- Loading the GPS-overlay-Chart for the departure Shows the waypoints perfectly matching with the Chart. Cool.
- ATC gives me the clearance with excatly that departure‌
- rest of the flight same problem as in case 1 with the direct-tos.

But what happens, when ATC does NOT give me‌‌‌‌‌‌‌‌‌‌ the pre-assigned dpearture?
On a GNS430 or their companions, I simply throw out the departure and throw in the new one.

‌Okay, that's for now.‌‌ Maybe there are good ideas how to handle this.

An don't tell me, SD is for VFR!. SD is far beyond being VFR-related only!!!‌‌

It sounds like you wish to insert a new waypoint into your route, rather than use Direct To which is for diversions and shortcuts. Is that a fair summary?

Tim,
Can you please publish a guide as to how you overlay STARS & SIDS on SD whilst flying  ( or planning ) 

I also have noticed of late that a lot of airfields are not visible  on the mapping screen when on a bigger distance scale !!!! if I am planning a long sector I like to put in a midway point & it isn't possible when on a bigger scale?  Is it a setting that I might have buggered up?

At least for ONE Airport (EDDV) I found a geo-referenced GPS-OverlaySID within SD that perfectly matched the clerades departure-route.
For STARs there may be similar mechanisms.‌

Sorry for the late answer. I think neither inserting a waypoint nor direct-to is the perfect solution for this. I may be influenced by the workflow a GNS4/530  dictates.

Typically we get an direct-to waypoint which may be part of the filght-planned-route (superseeding‌ a few waypoints) or may be completely off-route. At more or less late Point, I typically re-join my planned-route.
1. inserting a waypoint‌‌
 The direct-to waypoint inserted in a route generates bad looking hooks in the route as the new waypoint normally inserts between two existing waypoints. Additionally i do have to choose this waypoint from the pilot's log as a direct-to

2. simple direct-to
This kills all me pre-formed-route with all remaining waypoints which I may Need later on.

A possible solution can be having the route continously shown as planned in a different colour, while having another  ‌‌‌‌‌‌Magenta line which leads from the current Position to the direct-to

As an example on how to quickly process a ‘Direct’ or ‘Shortcut’ see the attached videos. It’s indeed not exactly the same logic as in a Garmin GPS like the GTN’s, but it works well.