I just installed AnkhSVN to have subversion support from within Visual Studio 2010. I noticed I had to go to Tools > Options > Source Control to select the current
There is unfortunately no good answer here. You will simply have to go in and manually change you visual studio source control provider settings before you open the project. This is a limitation of how this particular plugin system works, and will probably take a new version of visual studio to specifically address it.
This is an instance where visual studio works better for the enterprise shop with standardized source control tools, and not as good for a contractor working with multiple clients across an array of technologies.
Source control provider auto switching based on reserved directory presence can be done with a VS extension as described here.