Based on your description, it sounds like you have Stage 3s. It would be helpful to see a picture of them. One can read on the on the features section of the Elka for Spyders link (Click Elka vendor on homepage of Spyderlovers.com) that adjustable low/high speed damping isn't a feature until Stage 3.
My reservoir hoses remain inside the hollow of the A-arm, and as close as possible to the shock. This way, the hoze flexes unhampered along with the movement of the A-arm and the shock assembly while in motion. That's what makes sense. You don't want your reservoir hose outside the moving A-arm. Beyond being a hell of a reach for the hose, one 'snag' while ryding and you could break it. Then there's the SilverSurfer solution: My Can Am dealer had 'em on in 45 minutes as part of my 3K service. I pride myself as a quick read on the technology and tweaks of all this; but I like a qualified mechanic to do the major work nonethless. Again, just my solution.
Shock absorber covers: I wouldn't worry too much about that. These shocks fit a cross-section of vehicles, to include dirt bikes and ATVs. When I look online at shock covers, they mostly apply to off-road bikes, ATVs, etc. Elka does sell some covers, but they are pertinent to off-road stuff. Rain and paved road is not going to hurt your shocks. Your hose, mild soapy water and maybe a soft wash brush should do the trick.
Surfer