Creating Bubble Charts is one of the biggest challenges in Excel and Excel Services with respect to data visualization. Microsoft made it very intuitive in PowerView and very not intuitive in Excel. Frankly, the way this functionality is implemented in Excel makes it practically unusable. Rumor has it that this area is getting a lot of love and attention in the new release of Microsoft Office (commonly known now as Office 15) but for now we do need some help with building this in the Excel Services supported way.
Microsoft has posted an example of how to do bubble charts in excel so that it will be suitable for Excel Services. You can find a link to the excel file here. It took me a while to figure out how the file is set up. So to get a quick jump-start on it, take a look at all of the name ranges defined and also click the bubble chart and then on Chart Tools->Design-> Select Data button on the ribbon and then Edit on the Pop up Window to see how those named ranges are being used in the chart.
Not easy and user-friendly, but it works and will provide a much-needed relieve until the new features come out with the new release of Microsoft Office and SharePoint.