I'm doing research for a couple of years. I worked for the same people for years before I had DS, and figured we'd keep doing what we were doing (me there all the time) when I came back. My first day back, though, they told me I could work from home as much as I wanted as long as I was productive (and obviously there are some things that can't be done from home, so those I have to go in for). I love the arrangement; it lets me spend a lot of time with DS, minimizes the amount of time I spend driving/preparing bottles/pumping (ugh. HATE pumping). When I am physically there, there's a really good reason for it (taking care of patients, using software that can't be used at home, meetings).
My one piece of advice is to overcommunicate. When I was on site, I would just present my work when I had something pretty complete. Now, I send lots of "updates" just to let them know I really am working at home. When I go to a meeting, I make sure I'm visible (presenting or commenting) so that they know I'm still there. And so on.
As far as drawbacks, (1) DH assumes that since I'm at home, I'm like a SAHM... but I'm not, I actually have to work all day, so a lot isn't done when he gets home... haven't really worked this out yet, but he's pretty receptive and it's just a matter of reminding him from time to time; (2) I sometimes get confused on that issue, too -- I'm home, so I want to clean the kitchen and do meal planning, etc. I need to remind myself that I'm "at work" and just let that stuff go. On the other hand, things like playing with DS is the whole point of being home, so I take that time.
Another thing that really helps is childcare in the house. Three days a week we have a babysitter... if you're always going to be home, you could have just a mother's helper type person. It's hard to get stuff done if you're constantly being interupted.
Hope that helps!