I don't use Base Camp either, I use Map Source, but I've tried Base Camp. Are you loading the maps you download directly to the unit? Does Base Camp allow installing maps 'into' the pc-side software? (or just reading them off the unit?) If you load them into Map Source using MapSourceToolKit, you can still only view one map at a time, but you can view all the maps that you install (Garmin maps, overlays from here, maps you create yourself, etc).
From this, you can create Waypoints, Routes, etc. following the trails on the map. If necessary, switch between maps, but you can view any map that will be installed on the GPSr unit. I first create significant Waypoints, then create a route, making sure to click on map features for all intermediate points, and the major Waypoints. (Clicking the map features prevents new intermediate waypoints from being created at insignificant points along the trail.) Then when you navigate the route, it won't get stuck on an intermediate waypoint that you didn't get close enough to to 'pass', and will basically follow the major Waypoints.
On the Oregon, you have 'custom maps' which lets you upload geo-aligned image file maps to use on the unit. You can use Google Earth to crudely align (overlay) images, and I believe KMZ files are compatible with the Oregon. You can also use software (OziExplorer, GlobalMapper, others) to more precisely specify alignment points and georeference the images, ultimately transfering them to your unit.
Personally, my 'best practice' is:
I use what the Oregon calls Custom Maps to view a map in Map Source, create Waypoints and a Route. I hike navigating the route and viewing the Custom Map on my GPSr eTrex, saving a Track and more Waypoints (gates, trailheads, water, etc) as I hike. I save all this, and use my GPS-ed Waypoints to help improve the map alignment (replace the Google Earth visual-waypoints and re-align the map). I do all that because I'm using the maps and data to create local trail maps to share with this community, but without the map-making part, you could relax the 'best' practice to suit your needs.
I hope that helps, because I've been searching for my own map-making 'best practices'. Also, I keep a very organized folder structure to stay sane.
[EDIT: I just realized the Oregon's Custom Map feature probably isn't available in Map Source since this recent feature is likely only included in Base Camp. I use MOAGU, which is an older program that 'hacks' images to work on many Garmin units and is compatible with Map Source. (With some tweaking MOAGU can work with the Oregon/Map Source too) But all of my general email should apply to maps available on this website, loading them into Map Source first, then using that to load them to the GPSr unit]