Doing two 50% water changes would be only a 75% change in total, not a 100% change, so it would be better to do three or four 50% changes if you don't want to do one 100% change.
BUT... you really should just do a 100% change for the health of your fish.
I'm dealing with a fish-in cycle process right now, too. I made the mistake of ditching my substrate for something new when I switched my betta from a 5 to a 10 gallon tank and I lost the cycle. Apparently, the beneficial bacteria in the substrate is more substantial than I had been led to believe on various forums I'd read.
My ammonia reading usually gets up to around 0.5; once it was almost 2.0 and I have seen it at 1.0 a couple of times in the process. I do 75%-90% water changes daily, and sometimes twice a day.