OmniOutliner is an excellent tool, which I use for many things, but I'm not sure that jumping ship from Excel makes sense in this case.

Have you tried, for example, selecting the range to be formatted, and applying something like:

View > Formatting Palette > Number > Format:Custom ... > Type > #,##0.00;(#,##0.00)

(Where the second part, after the semi-colon, specifies the format for negative numbers)

?

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