That depends.
In Free Flight the starting position is determined by the runway's bgl file and the data entered by the designer. While not impossible to modify it is not something easily done.
In missions the starting position is defines in the mission's mis file. You can open this file with Notepad and scroll down to proper runway entry, usually [Runway.0] but not always. The line that is most important is:
takeoff_start_pos=-100,0
To adjust the takeoff point on the existing runway work with the takeoff_start_pos= section. A positive number represents the distance forward of the starting point as defined by the designer. A negative number represents the distance back from the starting point. This "starting point" is usually the center of the runway as with the stock airfields but not always. Some designers set the starting position at one end or the other. In the example above the starting position is 100 (feet, meters, yards depending on who you talk to) behind the starting point.
Here's the thing to remember. To give yourself a longer runway make the negative number larger (-200 above). To shorten your runway decrease this number (-50) above. If you are starting just off the end of the runway and the entry is -400, try changing it to -350 and start again.
Remember, any changes you make this way will apply only to this one mission. To change the starting point permanently open the airbase.dat file in the INFO folder and find the runway there. Make the changes described above and all subsequent missions will start at the new point. Existing missions will still start at the old location and must each be changed individually.