Hello. The above posters gave some really helpful advice, but I'll throw in my bit too. I finished my undergrad last May, and have applied to and will be attending a PhD program in the fall. During my undergrad, I had 2 years of research experience with an incredible advisor who encouraged me to give talks at professional meetings and submit manuscripts (currently have 2 publications in review from my undergrad thesis). Personally, I just felt like skipping my MS and heading straight to PhD was "right" for me. Granted, as some of the above posters have said, some people really regret skipping a masters... I'm hoping that's not me in the next couple years It's a risk I was willing to take.
If you don't feel comfortable enough with your research skills (expt'l design, grant writing, field/lab methods, and analysis) yet, then probably going the MS-first route would be a good choice.
As far as GRE's, I had mediocre scores on the general test (70th percentile across the board) and managed to get into my dream school, which is ranked in the top 10 for Ecology Phd's. So apparently mediocre is alright. One suggestion I have is to consider taking the Biology subject test. Only a couple of my schools required it, but I did really well (much better than the general test) and sent my score along to said dream school anyway. During my interview there, my future advisor said that it was very helpful that I submitted it, and that it kind of counteracted my blah general GRE scores.
Good luck with everything!