"Any suggestions on my splitting the days between Bruges and Ghent?"
Opinions about the "big four" in Belgium (Brussels, Bruges, Ghent, and Antwerp) are all over the place, as a search of the forum will show. My personal take (from 2002, when I was there) was that Antwerp was my favorite, Bruges was very nice (yes it's touristy, but particularly if you stay overnight, you can find the less crowded parts), Ghent took me time to warm up to but I enjoyed by the end of my day there, and Brussels I didn't care for, except for my wonderful Art Nouveau tour with ARAU: http://www.arau.org/en/tours. If I ever go back to Brussels, I'll plan my visit around ARAU's English tour schedule.
So, all I can suggest is you read as many opinions as possible, then plan to visit all four yourself (as you are doing) and form your own opinion.
"Using the Intercity train is the only way i know to get to the cities I want to visit. Is buying individual train tickets more economical?"
These cities are all connected by several trains per hour. The trains do not require advance purchase, so you can decide each day if you want to stay where you are or see another city. For example, if after 2 days in Bruges you decide you don't like it, you can take a day trip to Antwerp cheaply.
And, Belgian domestic trains go to all three Brussels stations, so you can get off at Central, which is indeed much closer to areas of interest than Brussels North or Brussels South stations. The train from the airport also goes to all three stations.