I don't think it's an issue to upload the two-page spread and then side 1 and side 2 separately. If you prefer to scrap double pages, then I say go for it!
__________________
Cassie
My Gear: Nikon D300s w/18-200mm VR & 50mm 1.4
Software: Adobe Photoshop CS4, PSE 10, Lightroom 2
