I hope I have understood it correctly - you can have two website with 32 bit dlls and 64 bit on the same machine. For this you can have respective JREs and DLL in the bin folder of the corresponding application i.e. - 32-bit website will have bin folder and in it a lib folder of all 32-bit Tridion JAR files and similarly for 64-bit application.
Moreover, you need to mark the following attribute in IIS Manager accordingly for the website:
In the Application Pool of the website, choose
Advanced Setting and mark the highlighted attribute accordingly:
For 32-Bit application, this attribute need to be set to