Sitecore 7.0 ECM - 2.1
I have a sitecore instance with multiple websites. I've installed ECM and I'm not sure what should I put in the Base Url field (/sitecore/content/Email Campaign). I've tried http://mywebsite1.com and it works. However for the other websites the url is something like http://mywebsite1.com/content/mywebsite2/page. I'd like to have my urls to point directly to the website - http://mywebsite2/page. Should I have something different on my Base Url? Can I configure this configured somewhere?
Unfortunately you can only have one Base URL per ECM Manager root.
You could create a manager root under each site though which might meet your requirements. This is the recommended approach for a multi site EXM set up.
Take a look at the documentation on creating a manager root: