If you don't see a progress bar when uploading files then you are not using NeatUpload and adjusting the NeatUpload settings won't have any effect, in that case the <httpRuntime element has the relevant settings. If you do see the progress bar when uploading then the NeatUpload settings are important, you might also try increasing the maxNormalRequestLength. Even when using NeatUpload the executionTimeout on the <httpRuntime element is a factor.
Hope that helps,
Joe