I had the same problem with Velvia 50. You could try Provia slide film instead. It has more latitude and produces very high quality results (superior to Velvia 50, but that's just my opinion)
Provia has no more latitude than Velvia - it just that it's dmax is a lot less and so looks like it does when placed on a lightbox.
Velvia 50 actually as about a 1/3 of a stop more than Provia but you need a drum scanner (and a good one at that) to get all of that shadow goodness out.
In tests, Velvia 50 has just over 8 stops of dynamic range. If you rate Velvia 50 at ISO 40 then the range goes from -6.333 to +1.666
In reality, the darkest couple of stops in the shadows suffer from colour shifts and can be very grainy - hence they should only be reserved for 'tonality (a textural black). so when you're metering for a drum scan I would use -4 to +1.666 (for a typical ccd scanner I would say -3 to +1.666)
So, find the highlight that you want a little texture to and place it at +1.666 and then meter your shadow. If your shadow is too dark you'll need to grad the highlight somehow. If you want a nice looking transparency you can then check the placement of tones around your image.
WARNING! Velvia 50 has an odd behaviour for it's different colour layers. The yellow layer doesn't go transparent until about +3 or even +3.5. Hence you can get away with a lot more headroom in the areas around the sun on a sunset. Blue is the opposite. A blue sky haze really needs to be placed at +1.5 or even +1.33 as when blues get over exposed they shift to horrible cyan quite quickly and blow out to clear very fast.
p.s. when spot metering shadows you have to realise that when you take a shadow reading you're normally taking it from a textured area and will get an average reading of that area. The actual blackest points of the area may be one or even two stops darker than the average. I tend to walk up to my subject (or an area like it) and actually stick my meter into a shadow - or failing that I make my own shadow on an area. The same goes for highlights - what you read from a distance is a textural average. When you meter it up close the actual highlights of the texture may be a stop brighter.
p.p.s bellows factor works in reverse. If you have a shot with the horizon in the middle and you have a close foreground which you've tilted to get in focus, not only do you need to expose more for the foregroun because of the bellows factor, you also need to expose less for the sky because it's focussed 'past infinity' ("to infinity and beyond!")