You need to register you game within Impulse to your Impulse account. Once you are signed in, go to the "My Games" tab. At the upper right, there should be a register product button. Click it, enter the serial number, select the games category and find Sins of a Solar Empire from the list (whatever version you purchased). Hit add registration and you should then see Sins of a Solar Empire in "My Games", where you can then click on it to see an update button on the lower right.

I am also planning on purchasing from a brick and mortar store, I have internet access through many means except my gaming rig.  Am I able to download to my laptop and transfer the updates via flash drive to my gaming rig?

edit: supplementary question, am I able to down specific updates (ie, diplomacy 1.21 instead of 1.3(1)) so I can use some of the mods available?