It took long time - a day - with partial transfer of data, I need to transfer remaining data. How to transfer while iPhone is already in use for sometime?

As that app requires the phone to be in setup mode you would have to completely wipe the phone and start again.

You would lose any documents and photos etc you have created since you set it up first, unless you import them to your computer or cloud storage.

Settings, General, Transfer or reset iphone, Erase all content and settings.