I am with Peter Apps on this one. A manual injection seems to be one of the simpler options.
Assuming you have Chemstation running your Agilent GC, load the appropriate analytical method. Clicking
"instrument -> select injection source" will allow you to select the column you intend to use (front or rear), and also allow you to change the injection source to "manual".
Next, click "run control -> sample info..." and enter any pertinent information such as sample ID, ISTD amount, mulitplier(s), etc, under the "sample parameters" portion of the box. When finished, click "Run Method" at the bottom. (A few other ways could accomplish this also; chemstation software tends to have that caveat).
The tower at that point would normally engage to run the sample; however, you have now changed it to a "manual" injection, so this will begin bringing the conditions of the instrument to the methods parameters.
***Wait until all parameters have gotten to their setpoint. *** (oven temp., inlet temp, pressure, etc) The "Chemstation Status" box should have "Run in Progress" in dark blue; and "Waiting for injection" in hot pink.
Lastly, prepare to inject the sample, remove the tower so that you will have access directly to the inlet. You can simply use the same auto-injection syringe installed on the tower to inject the sample. Basically go through the same steps the tower would have in regards to how it gets ready to inject a sample (rinse the syringe a few times with your rinse solvent, and a few times with the sample). With the appropriate amount of sample pulled into your syringe for analysis (depends on your method; 10 microliters is common), place the syringe needle through the septum nut at least 4/5 or so of the way, and inject your sample. Immediately after doing so; press "Start" on the GC keypad to begin analysis.
Hope this helps

Bret