To get the Plugin, Go to File > Plug-ins > Install Plug-ins, find "Notes and Rests," and install "Merge To Voice 1".
The new Sibelius staff decondensation features for parts can cope with notes on the same stem. I don't use a version that has this, but this is my understanding.
You said you are already manually merging, so "chords" is the end result of that process in any case, which is why I suggested you begin that way at note entry.
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