Generally, you download the latest update(s) from the Lionel site:
https://www.lionelsupport.com/...roductNumber=6-14295
...which you find by going to Lionel.com and clicking on Support, then selecting Service Documents, then typing in 990 which brings up the update links. Lionel's website needs some update itself actually .
Next you download the update to your Windows computer, storing it on the file system somewhere.
And then, bring up the LSU, connect your base either with a com port (or wifi if you have the LCS wifi module). The options are then available to write to a Lionel black module(s) using the port on the Legacy base. You can write either the base or handheld update to the module(s) this way. Then you use the module(s) to update the base, or to update the handheld following the instructions in the Legacy manual (holding a button and turning on the base or the handheld with the module inserted). The modules are repeatedly writeable. You only need one. These modules are not USB modules but are similar to the orange modules that are sent with Legacy engines, etc.