I believe you can still use Innovus - you will have to have LEF models for these other blocks, or if they really are black boxes, they can be defined as such early in the flow, but you'll want LEFs for them eventually. not sure if this answers your question or not. Blocks (not std cells from a library) are referred to as either blocks or macros and are represented in the database by a LEF for physical info and .lib files for timing info. There should also be a GDS of a block that will get merged in when the final design is written out as GDS for tapeout. Hope that helps....
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