I have done it by creating a mash profile with a 'decoction' step, which I relabeled 'carmelization'. The temperature can be adjusted to pull about the amount of wort for the reduction in proportion to the volume of the infusion. This will not account for the volume loss, but I generally know having done this several times how much volume I will lose and adjust this in the "mash tun dead space". You then need to adjust the brew house efficiency to match the reduction effect on the pre-boil gravity.
Having said this, it is much easier just to put in the step and ignore the numbers for volume loss and dead space. Instead, I use my standard profile, remove the first 2 liters of run off, carmelize this and then add back water to get back to the volume I pulled. This does two things, it keeps my volumes pretty consistent, negates most of the color increase from 'carmelization', and simplifies having to got back into the equipment and mash profiles to adjust everything. Additionally, the water added to the 'carmelized' wort will thin it out to pour back into the main wort and help rinse the bottom of the pot.
The first time I did this, I ended up with a thick paste (since true carmelization requires bringing the temperature up above boiling, there is no free water to allow for fluidity of the wort) and had to scrape the carmelized wort from the pot.
I have to admit that I dislike the term 'carmelization' since what we are really doing is reacting the sugars and proteins to create complex melanoidin flavors in the wort. This is also what really produces some of the 'smokey' flavors attributed to the Scottish and wee heavy beers in combination with the particular yeast strains used.