The most important thing you need to know at this point is to NEVER install or remove a tuning device from the EEC with the vehicle's ignition switch turned ON. Always make sure the keys are in your hand, on the floorboard, in your pocket, or anywhere else other than in the ignition switch before installing or removing a tuning device from an EEC still bolted to the wiring harness. Installing or removing a chip on an EEC while the ignition is ON is a sure way to fry the EEC and possibly the tuning device along with it. So do NOT take short-cuts and think it is safe to disconnect or connect the tuning device in this fashion. Obviously if the EEC isn't connected to the vehicle wiring harness, you should be safe. Once the TwEECer/QH has been installed onto the EEC, connecting the USB cord to the laptop can be done with the ignition ON or OFF.
The next thing to know is most any tuning device you buy NEW will be delivered blank. That means there's no tune in its memory. If installed in this state, the engine isn't going to start. And in the case of older EEC-IVs, you'll likely also notice the fuel pump runs constantly. To correct this, write a valid tune to the device. If you don't have a tune in-hand to write to the EEC, you can start with your EEC's stock tune by reading it into your tuning software. Refer to the help files of whatever software you are using for details on exactly how this is done. If you are using a TwEECer or Moates hardware, I highly recommend you use BinaryEditor (BE). Regardless what software you are using, you'll 1st need to know what strategy your EEC follows. To figure that out, read this FAQ:
What strategy does my EEC follow?
Once you've identified your strategy, load that strategy into your tuning software and then read your EEC's stock tune OR use a supplied tune file that is likely available where you found your strategy file. I highly recommend you use BinaryEditor if it has support for your EEC. The BE installer can be found on the download page of the EEC Analyzer website:
EEC Analyzer Download Page
On that same page, you can find folders with strategy names. The folders contain the relevant definition (*.xls or *.cry) and tune (*.bin) files associated with that strategy for use in BE. So if after installing BE, you find your strategy got installed, but there are no tune files in that same folder on your computer, you can download all the known tunes for that strategy.
All strategies that have *.xls def files are open sourced to the community. However encrypted *.cry def files require you license its use with the def file's author.
With BE installed, registered, and loaded with your strategy and tune files, you can now write that tune to all tune positions on your tuning device. For details on getting BE registered, read over this FAQ:
Keep in mind you can write tunes to either of these hardwares WITHOUT them being connected to the EEC. During the early days of getting started, it is more convenient to work with the tuning device stand-alone instead of in the car's EEC. While connected to your laptop stand-alone, you can confirm correct hardware driver install, software install, software registration, and proper hardware/software communication. Get a working tune written to all tune positions in the tuning hardware before installing the tuning device on the EEC.
All TwEECer tune positions are controlled via the supplied hardware switch. BE has no feedback as to what tune position you are in. However some strategies may let you datalog tune position if you desire. There's a Getting Started document that is available, written with TwEECer users in mind, but may also be useful for others. Much of the info covered in this document is also covered in the Glossary Of Terms Used in EEC Tuning which is both an introduction to new words and terms you likely aren't familiar with as well as a review of many generic terms you likely already know.
Tune position control for the Quarterhorse is more involved. Refer to BE's helpfiles on Moates Hardware for more details on the various Modes available for the Quarterhorse.
Another very important topic you should be aware of is how to rescale tables in your tune. Learn how here:
What are Scaling Functions?
This is a rather advanced topic and may be one you read, don't quite get the 1st pass, then need to read again later. It also helps if you've had a little tune-time in the tune editing software to be more familiar with what tables and functions look like. If your first pass through this topic seemed over-your-head, let some time pass and try reading it again. Understanding Scaling Functions is one of the fundamental concepts to being a successful tuner, so don't assume you don't need to know about it.
At this point, the other FAQs on this site and the helpfiles in BE and EEC Analyzer (EA) are your next best sources to getting educated on what EEC tuning is. I highly recommend you read through both BE and EA's helpfiles. EA's helpfiles, in particular, cover just as much on tuning concepts as they do how the software works. Many many questions people have about how to use BE and EA are answered in their respective helpfiles. It's amazing how difficult it is to get people to actually read them. Also if you find errors, typos, or some issues with them, feel free to report them either here on this site or to the developer, Clint Garrity (86GT).