Yes, as others have stated the SCTuner software and the SCT software are totally different. I should have clarified. The SCT software is more expensive but you can do more with it. The binary is decoded better and there are more parameters that you can change. As Dave said, the SCTuner software is rather old, and works off a spreadsheet format. You can download a trial version on SCTuner.net. This software WILL work with the EEC tuner. As some of the grpahs are useless, I find the interface much much better than using a text based format, and some of the 2D graphs help such as the MAF transfer function.
Again, as Dave stated, all software works off of the same parameters, (tables, scalars, and functions). When I orginially bought my tuner, the SCT package was fairly new and expensive so I stuck with the EEC tuner. For most people, you can get a great tune with using the EEC Tuner and any software that applies.
What I change the most is my transfer function to match my fuel tables. This way, when I command a 12.2 ratio, I better see a 12.2 ratio on my wideband, and if not, then I modify my MAF functions at certain voltages until I get what I'm commanding at a given load value. Keep in mind that this only lets you see the upper end of your MAF curve, somewhere around 2.8-4.8 volts.
When I tuner the lower half of my curve, I turn off adaptive control, drive the car around and log my AFR under light loads and idle. Adaptive control is basically the closed loop function that adjusts fuel, spark, ect by feedback from the stock O2 sensors. You could be running around 20% rich/lean, and the car would adjust for that and still show a 14.6 ratio during idle, or light loads. Turning it off basically lets you see how the car is running without adjustment paremeters. I turn it off, and set both of my fuel tables to 14.6 under all load conditions. This is to assure me that I am always commanding 14.6 regardless of loading conditions just for the purpose of tuning.
There is a lot to tuning as I'm sure you're aware of, and the only way to get good as it, is to read read read everything you can off of the net. It took me a good 3 months until I knew how to do a basic tune with and understanding of all the functions. After a good 4+ years now, I can tune most fords with either the EEC or Tweecer in an afternoon with great results. I must stress this point however. DO NOT change any other parameter until you get your MAF curve perfect. Don't start changing spark vaules or fuel trims until you get your curve at a point that when you command a fuel ratio, you should be getting that fuel ratio.
I got my PLX for $500 at the time. Which was a good price considering you have a logger and a wideband until. I believe they now sell a R-500 unit for $580 now. A lot of people go with the Inovative Unit, and while it's nice, I like the functionallity of the PLX until. Again, at the time when I got mine, they only had the LM-1, which was a huge hand-held unit that needed power inputs and had limited functions and expensive harnesses to you needed to buy in order to data log. I wanted a permanent mount, with datalogging and PLX was the best option at the time. I'm sure Inovative has much better stuff out there now. Shop around and see what you can find.