Туда, где я должен указать на корень VCS TeamCity?

I would recommend using http://obfuscatedserver/svn/main/ as the VCS Root, and then restricting which folders are checked out using checkout rules.

Add the following checkout rules (section 2 of the build config):

  +:/MyProject1/trunk

You will probably also need to update the location of your msbuild file to

  MyProject1/trunk/MyProject1.proj

and set the working directory to

  MyProject1/trunk

This does seem like a lot of work, but next time you want to add a new build, you don't have to create a new VCSroot.

However, the real benefit comes when TeamCity polls your SVN repo. Polling your repo once will discover all the changes for all your builds. This is especially important if your repository is hosted somewhere like sourceforge or googlecode. You certainly don't want to be polling their servers for every build you have configured.

Also, if your repo is hosted by a third party, you might want to set the vcsRoot's Checking interval to once an hour or similar. You can always ask teamcity to check for pending changes from the actions menu on any of the build overview pages if you can't be bothered waiting for the hour to elapse.