What ReSharper does is that when it has an option that conflicts with the default Visual Studio settings, it installs a marshal that when you choose the option, asks you which one you want to win. That gives us an option.
The option would be to find out what options conflict between these two tools and do one of the following:
Implement a marshal that asks you which option to choose or, the one you probably prefer
Force the action of this option to the tool you prefer.
It may be possible to device a macro that performs this job. To implement such a script, it's important to know what type of options are conflicting. Are you talking about shortcuts, menu options, toolbar options? With this information and your Visual Studio installation, it should be possible to automatically update all the options and pick the one you want.