Hi, also have had some problem some monthes ago - I created separete component ProductCatalogSimpleIndexingAdminSecond. After that one of my colleage gave me some advice:
The creating separate component like ProductCatalogSimpleIndexingAdmin for the second IOC is possible way for resolving your situation. But I afraid that this way will be required creating mane duplicates for already existed components.
In my opinion the better way is the following:
starting from AssemblerApplicationConfiguration and ApplicationConfiguration component. It contains details for connecting between ATG and Endeca. Of course you should configure different components for different Endeca Apps.
Find all components that uses AssemblerApplicationConfiguration and ApplicationConfiguration. Customize these components for using one or another *Configuration component depending on what index works. (many variants released it: the most simple global custom component with flag.)
Then customize the existed ProductCatalogSimpleIndexingAdmin. Using one or another IOC and setting the flag in global custom component when index started. You can add some methods into your custom ProductCatalogSimpleIndexingAdmin like:
Execute baseline index for both IOC (one by one)
Execute baseline for IOC 1
Execute baseline for IOC 2.
Note: you should be afraid about incremental (partial) index in this configuration. But resolving conflicts in incremental index should be done after full implementation these changes.