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Hmm. You should have a Partition called Top automatically, and after compiling a post-fit netlist already exists for it. (I assume Incremental Compilation is on, but it's on by default and you'd have to go out out of your way to turn it off.). Then just set that Top Partition to Post-Fit, add your signaltap, which again is automatically a partition although it won't show up as one in the Partitions Window, but you will see it in the Incremental Compilation sections of the output reports.
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I believe the problem is the original design settings had incremental compile turned off. I am having to use an old tool version (Quartus 6.0) due to presence of Nios & avalon switch fabric in the design (from past painful experience, I avoided upgrading to a newer tool), so maybe the default is off for that version or the original designer turned it off.
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