You can still use QuickBooks or other applications while your company file is uploading or syncing. If you change QuickBooks data during this time, the changes will be reflected in your online services the next time you sync your QuickBooks data. The performance of QuickBooks shouldn't be affected during the initial upload, but online applications might run a bit more slowly.
Don't turn off your computer or disconnect from the Internet during an upload or sync. Because the initial upload can take a long time, make sure to do this at a time when you can stay connected.