I've basically been following this diet and was wondering if it's still fine to have the carb up on Thurs even if I'm only doing cardio that day.
I do a 3 full body M/W/F and cardio Tue/Thur/Sat. http://www.bodymusclejournal.com/vol02/holy_grail.html

The title kinda tells the story. The diet, I feel, is really helpful for beginners and beginning the dieting change or route. If you've mastered the diet, kept from sugar cravings, regardless of the type of workout, so long as you are averaging total calories to be negative, the diet will work.

The Monday/Thursday is really just saying 3 to 4 days, have a carb up meal. Monday/Thursday did not work for me, so I changed it to Wednesday/Saturday.

I see what you are saying, but what type of cardio are you doing? If you feel better to do a carb up after lifting, then do so on Friday, keeping a M/F routine.

The carb up is mainly to be an activator to your metabolism, kind of a kickstart to rev things up.

I'm doing 30 min SS cardio 3x a week right now.
I've been doing this diet for almost 6 weeks and have lost inches, not so much on the scale.
I was doing the Anabolic Diet before this so this was not hard for me to start.
I like carbing up a couple times a week rather then an entire day; I feel better.
Should I still carb up using my last meal of the day even if I train in the morning or does it matter?

It does matter according to the design of the diet to make the carb meal at the end of the day. No supplements are to be taken, too.

Aram had a great post about why it is best, relating to sparking the thyroid, etc.

I agree with Frank, the day does not matter as long as you have 3-4 days in between. I always have my carb up meal the evening before my hardest, heaviest weight training on Tuesday(Legs) and Saturday(Back). I feel I am able to to train those large bodyparts optimally with a full carb load. Hope this helps, try various schemes and see what works best for you.