Here's a surface-level rundown, let me know if there is something specific that isn't working for you...
Open BrewTarget, click the blue "+" button on the top left for a new recipe.
Enter the name, click OK.
In the middle of the screen, you'll see fields for "Target batch size" and "Target boil size"
Enter 2.5 gallons for target boil size, and 5 (or 5.5, or whatever your target batch size is) for your target batch size
Enter your ingredients using the different tabs (fermentables, hops, yeast, etc) and double-click on the "Amount" field to enter the amount you are using.
That should get you pretty close. You can get into setting up your equipment profile to help fine-tune the results. Does that help, or is there perhaps a more specific part of the process that isn't working for you?