ballyboley,
The first two situations you ask about require what are called 'conditional waypoints' & unfortunately can't be entered by the flight crew. They can only be entered into the database as SIDs or STARs by the powers that be.
Regarding the third question, you should be able to enter the runway threshold as a waypiont in either the legs page or the fix page, eg. RW19 (it might be RWY19 - my memory is getting a little dim!). When you type this in you will get a number of waypoints to chose from, particularly if there are a number of airports in with the same runway direction in the area, so be carefull to get the correct one. They are listed in the order of closest one first. If you are close to the airport, the correct one should be at the top. Then, on the legs page you then put this point to the top of the page (if you didn't enter it there in the first place) & type the inbound track into the bottom right corner. On the fix page just put the reciprocal track in as a radial.
Sorry, I don't know the answer to your last question, but if I remember rightly, all the user defined waypoints are cleared after landing - not sure though!