The lastest beta introduced a few FMS screens in the Q400: one of them is the flight plane page (FPL). Instead of using the Navigation page to enter the plan into the FMS it's much more fun to enter it manually! Because not everyone might know how the FMS works in this regard here's a short tutorial showing a few possible options to get things done.
To plan the flight you'd best use the Navigation page anyway. After planning the flight erase the plan again by clicking on the circular icon in the top right corner: this way the FLP page of the FMS will be empty once you enter the cockpit. Using the FMS to enter the flight plan isn't easier but more fun! 
This is the short plan I created for this tutorial:
We'll fly from KKIC (Mesa Del Rey) to KSFO (San Francisco). When you create a plan in AFS2 the sim will add an automated waypoint after the departure runway and before the arrival runway. Make a note of all waypoints but remove those automatically added points! I wrote this on my piece of paper:
KKIC runway 29
UAD (this is an NDB)
SJC (this is a VOR)
KSFO runway 28R
Now remove the plan from the Navigation page and step into the Q400 cockpit. The FMS should look like this:
We are at the FPL page already and the first field is ready for input. There are two ways to enter data into each field: you can type it in or select it from a list. We'll start with typing.
1. Type KKIC and press ENTER
2. Type UAD and press ENTER
For the next waypoint we will use the list option: using the list you can enter VORs, NDBs, airports and more: make sure you know what kind of waypoint you are looking for because you won't find a VOR in the NDB list which is why I wrote this down on my piece of paper.
3. Press LIST and then press the LSK next to VOR (top right LSK): you will see a list with VORs beginning with the one closest by
(LSK stands for Line Select Key: these are the buttons to the left and right of the FMS screen)
4. Press NEXT until you see SJC in the list (it should be number 12 on the second screen)
5. Type 12 and press ENTER: SJC will be added to the flightplan
6. Type KSFO and press ENTER: we also could have used the LIST option for this (KSFO would have been number 41 on the 6th page!) but typing waypoints and airports usually works quicker: using the list is simply fun to do sometimes.
Now we will select the departure and arrival runways
7. Press MENU
8. Press the LSK next to DEPART: you will see a list of all available runways
9. We want runway 29 which is number 2 so type 2 and press ENTER
10. Press the LSK next to FPL which will bring you back to the FPL page: the correct runway will be entered in the plan: you can check the heading and AFS2 will have added an automated waypoint in between the departure airport and UAD
11. Press MENU and then the LSK next to ARRIVE
12. Runway 10L has been entered automatically by AFS2 but we want runway 28R so press the LSK next to 10L: you will see a list of all available runways (if there are more runways they may not fit on one screen: in that case use NEXT and PREV to see the rest of the list)
13. We want runway 28R which is number 2 so type 2 and press ENTER
14. Press the LSK next to FPL and you will see runway 28R has been added to the plan: AFS2 will automatically add the final approach fix into the plan (which is always placed 10 nm out of the runway in the runway heading)
15. Press the NEXT to see the next page of the plan
Press PREV to go back again or NEXT to cycle through all pages of the plan. You can also press FPL to do this.
That's it! Now you know how to enter a flight plan manually into the FMS and how to use the LIST and MENU options to add waypoints like VORs or NDBs and even airports and how to add or change departure and arrival runways. This way you can change the arrival runway even during a flight!
Take note that the plan in the FMS is linked and 100% the same as the one on the Navigation page so if you can't get things done using the FMS you can always go to the Navigation page and edit/change things there.
PS In the real world FMS whenever you type in an airport or waypoint you will get a screen showing you more information about the airport or waypoint so you can check if you are entering the correct one: you have to acknowledge that screen before you can enter the waypoint into the plan. The current FMS in AFS2 doesn't yet do this. Maybe in the future.
EDIT
Somehow one of the images is repeated below (the one from step 14): don't know why or how to remove it but you can disregard it.
Did you copy the line from my post and paste it into the Search field of notepad or did you type the line...? You should copy it so it matches exactly: add just one space and you won't be able to find it. I found the proper line in your q400.tmd immediately after copying the relevant line from my post into the search field.
