I have my system running on an assumption of every flight being flown at 3000ft. As a consequence, I presume, the winds aloft are also for 3000ft.

Now I'm struggling to find the right button(s) to press and set it at 1000ft.

Somebody please remind this numpty

SD and a cheap Chinese satnav = Jobzagoodun.

The wind arrows shown on the main map are for one altitude only, so they won't change if you just change the level for one leg of your route. If you set the "main" level for your route (in the Flight Details window) that will update the level for which the wind arrows display data.