I think there should be a function in which you can paste notes/effects/whatever, and rather than simply replacing what's there, it overwrites only that data which falls on the same row/column.
For example, say my Square 1 looks like:
00 |D-3-01
01 |D-3-01
02 |------
03 |G-3-01
And Square 2 looks like:
00 |F-4-02
01 |------
02 |E-4-02
03 |F-4-02
If I copied those 4 rows from Square 1 and used Paste+Merge to paste them at Square 2, it would look like:
00 |D-3-01
01 |D-3-01
02 |E-4-02
03 |G-3-01
See? Row 02 is unaffected, as it contained no data in Square 1; effectively the two have been "merged".
This would be extremely useful in situations where, for example, you need to briefly interrupt one channel to play a 2-note chord.