Suppose you have a road bike with a top tube a bit short for you. The handlebar-to-seat distance should be about 25mm to 40mm (1" to 1.5") longer.
Where did you get the idea the top tube is too short? I'll presume you are comparing this bike (bike A) to another one, that fits you better, and has a longer top tube (bike B). Correct? If so, then...
STEP 1. put the two bikes side by side and compare the seat tube angle, the head angle, and the fork offset. If Bike A has a steeper seat tube, then you should put the seat back farther to replicate the Bike B fit. That done, move the handlebar forward on Bike A to replicate the Bike B fit. Once you have the same relationship between the crank, seat, and handlebar on both bikes, you have done all you can do without changing the frames. The two bikes presumably still have different head tube angles and different degrees of fork offset, though.
STEP 2. get the bathroom scale out, make a stack of books the same height as the scale, put one wheel of Bike B on the scale, the other on the stack of books, and sit on the bike on the position you are trying to replicate. Note what the scale says. Now turn the bike around so the other wheel is on the scale; note what the scale says. Now put Bike A on the scale and do the same thing. If you get radically different results, you may want to change the stem and seat position to get the correct fore-aft balance.