First, make sure you have all of your water losses for dead space and trub loss correct in your mash profile.
Second, you say that you got 'roughly' a 5.5 gallon batch and collected 1 gallon more wort. You will need to be more precise if you are going to get the software to better predict what your process produces.
Third, Volume losses occur in other places than grain absorption. You have dead space from your mash tun, boil off rate, loss to chiller and trub (your ~1 gallon extra wort), and any sampling loss both before and after brewing. You can make a preliminary adjustment based upon your initial brew, but I would recommend carefully measuring the volume of water in (both mash and sparge), volume collected before boil, post boil volume, gravity pre-boil and gravity post boil. From these you can calculate the losses in your mash tun (water in - volume out [corrected for temperature]) to give you your grain absorption. Then you can figure out your boil off rate (pre-boil volume - post boil volume -- both corrected for temperature). As an added check to your figures, your pre-boil gravity points (volume x specific gravity) should be pretty close to your post boil gravity points (same calculation). Mine usually come out within 1%, which is about my measurement error.
The boil off rate you can adjust in your equipment profile. The grain absorption rate can be adjusted in 'Options' >> 'Advanced' >> 'Grain Absorption'.
I would check these numbers over the next few batches and then make an adjustment to both based upon either the average for the batches measured or the median value for the batches measured, which is better to use if you have one skewed batch.