The update firstly downloads the data from the server onto the host machines hard drive - at this stage the speed is probably determined by the Garmin servers, best to avoid doing updates as soon as they become available - every device on auto update is accessing the server.
Once the file is downloaded the status bar gets to 50%. If the files have been previously downloaded the progress to 50% is very rapid, the host computer just checks it has all of the files it needs. If the download is interrupted it will resume where it got to rather than starting from scratch.
Then the files get transferred to the device via the USB cable, then back on the internal bus to the memory card. The Garmin 1000 has a pretty slow version of USB interface, don't worry about using a USB 3 port on the host, but best to avoid going via a hub if possible.
To get the edge 1000 to recognise the new mapping you must "eject" the device properly from the host.
The memory cards mapping has a device specific unlock code, it will only work in the device that it was created on (copying of the SD card for another unit using the SD slot in the host doesn't work, but is a very quick experiment that proves the limit is the Garmins usb speed!).
Cloning the SD card to create a spare or higher capacity SD card for use in the same device does work (not tried copy of files, only tried cloning).
If the host computer is short of space on the hard drive you may want to look into purging older versions of maps etc from the Garmin downloads (ProgramData>GARMIN>CoreService>Downloads>).
Edit: to add some real world numbers, they are from a different device (eTrex 30x) but look very familiar from my edge 1000's.
download of files from Garmin to host speed of 3.6MB/s (correlates with approx 30Mb/s of my broadband service).
copying files to device - this is the killer, started at 560ish kB/s, then as the unit runs out of memory it slows rapidly.
For non computer trained - B/s is 1/8th of the b/s (Bytes vs bits)
If you use an oversize card with significant spare capacity the Garmin has more room to do its housekeeping during the copy to device/card and is therefore faster (eg use a 32G card rather than 8G, but check the max supported by the device).