The quick answer is that your Legacy 990 set should have a cable that connects your computer to the 990 base. Also needed is the optional black module which you can purchase or do a search on the forum to find out how to convert your existing blue module so that you can download to it. Once you have the black module or the converted blue module you can insert that module into the base unit to download the latest legacy version for the base unit and the cab handheld. This is just a brief overview, further info can be found on the Lionel website where you also need to download the proprietary software to your computer inorder to perform the aforementioned downloads. I am sure others will chime in if you have further questions.
just a further note, Lionel is releasing a sensor track in the future whereby all information regarding a Legacy train equipped with its own individual sensor can automatically upload its info to the Legacy remote without going through the hassle of the modules
There are also some great Legacy instructional videos on the Lionel website
hope this helps,
Pete