There are 3 ways of running MDT with different than default JRE:
1. Run eclipse.exe with -vm parameter and specify location of appropriate JRE e.g.:
eclipse.exe -vm "C:/Program Files/Java/jre1.6.0_03/bin/javaw.exe"
2. Copy particular JRE (i.e. jre1.6.0_03 from C:/Program Files/Java standard installation folder) to Eclipse directory. After that you have to rename it to jre. During startup Eclipse will consider JRE files from this directory.
3. Add a switch with path to a particular JRE in eclipse.ini file. For example:
-vm C:/Program Files/Java/jre1.6.0_03/bin/javaw.exe