I presently do all of my creative endeavors (art, music, writing) under one brand, at least on twitter. I have a couple of separate facebook pages, but I don’t really push people to those, so they aren’t doing anything. It’s been working pretty well for me, but I can see the merits of having it separate. I probably won’t split things out at this point unless one area really breaks out where it becomes more of a sole focus.
I build my own sites and use virtual servers, but one thing I do to mitigate any potential storage issue (or bandwidth issue) is putting all of my actual art in an Amazon Web Services S3 bucket. That way I can keep my actual site code running on a very trimmed down, inexpensive machine and the storage/bandwidth for the heavy stuff separate. Since you only pay for the bandwidth and storage you actually use, it’s very cost effective and scalable.
I love Manga Studio. I still do a mix of pen & ink and digital comics and for the digital ones I almost never use Photoshop at all. Before I was in photoshop for everything or occasionally Illustrator. Once I get a Yiynova or a Wacom, I’ll probably do everything digitally.