For the flare, I cannot help because I don't really understand what you are referring to.
For lining up with the runway, there are three possibilities: with the instruments (ILS), with the GPS or visually.
- with the ILS: This is used at major airports during IFR flights (with the ATC guiding you etc...). The runway you are assigned to for landing has a ILS frequency (you can find it using the map and clicking on the airport) and an ILS heading. You must enter this frequency into your NAV1 radio and enter the heading in the appropriate instrument (somebody more expert than me will tell you the exact name). Then you must have a look to the line that is moving left to right on this instrument, when it's perfectly in the center, that means that you are lined up with the runway. If it's on the left, that means that the correct trajectory is on your left, so you have to slide left a little bit.
- with the GPS. The runway appears on the GPS, so you just have to make a turn far away enough, the direction to follow will be easy to determine on the screen.
- visually: take a look at your runway, first of all you must determine in which direction you have to land. Then, just draw a line on the ground that extends this runway (I mean, imagine it) far away enough, and choose a point on that line to make your turn toward the runway, you should then be lined up enough
