IF its anything like my 98 ex, your best option to do it yourself like i did is to first remove the door panel. then remove the screw that keeps the front track in place. After you have this screw removed you will need to get the window as high up as you can without pushing it too hard.
Then put your hand on the track and reach up as far as you can go. Next you need to use a finger to spread the track open where your hand is, and slowly use the window button to move the window down.
As the window gets near where your finger is you need to push the rubber out enough so that the window can slide back into the track. After you get the window on the inside of the rubber up top move it down more and keep sure with your fingers that it stays inside the rubber track until you reach the bottom. Then screw the track back in the opposite of the way you took it out. Notice the hole for the screw is oblong allowing room for adjustment.
You want to adjust it as far towards the back of the car as you can without putting excess pressure on the door and making it harder for the window motor to push it up.
If you have ever had a seat belt that was all twisted the wrong way and you folded the belt in half while pulling it through the upper loop by the roof to get it to flip over to the correct side the concept is pretty similar to what you are doing here. Simply forcing pushing one of the rubber guide edges out forcing the window to go over it and back into track.
It took me a few tries the first time but you will get the hang of it.
Good luck!!!
Aligning a driver side window on a 1998 Honda Civic requires the removal of the door panel. With the door panel off move the window until it can properly align to the track. Once aligned slide the window into place and reinstall the door panel.
The front track of the 2006 Honda Civic is 4 ft. 11 in. (59 in.).
The rear track of the 2013 Honda Civic is 4 ft. 11.9 in. (59.9 in.).
The front track of the 2007 Honda Civic is 4 ft. 11 in. (59 in.).
The front track of the 2014 Honda Civic is 4 ft. 11 in. (59 in.).
The rear track of the 2006 Honda Civic is 5 ft. 0.1 in. (60.1 in.).
The rear track of the 2003 Honda Civic is 4 ft. 9.9 in. (57.9 in.).
The front track of the 2003 Honda Civic is 4 ft. 9.9 in. (57.9 in.).
The rear track of the 2008 Honda Civic is 5 ft. 0.1 in. (60.1 in.).
The rear track of the 2014 Honda Civic is 4 ft. 11.9 in. (59.9 in.).
The front track of the 2009 Honda Civic is 4 ft. 11 in. (59 in.).
The rear track of the 2004 Honda Civic is 4 ft. 9.8 in. (57.8 in.).