Question: I have a scatter chart with a series of numbers in Excel. Most of the time, those numbers are high (>1000). I would like to display the scatter chart with those numbers in the default color, but if the number is < 1000 then display those in red. So essentially I want to highlight just those.

Answer: 
Plot the high and low values from separate columns (or rows):

![Simplified scatter chart with 'highlighting'](https://i.stack.imgur.com/dyLJ4.jpg)
The data point shapes and their colours will probably need to be changed if you want red + another colour and a particular shape but now each 'series' can be selected separately (by clicking on one of the data points from each 'series', in turn) and formatting to suit. I take it that *how* to format (described all over the place) is not a required part of an answer to your question.
Excel doesn't support 'conditional formatting in charts'.

If you can't plot these numbers in separate series (as per pnuts solution) then another option is to manually colour each data point (right click|Format Data Point) as long as you don't have too many. This is a hassle though if your data changes.