Hi Emily,
Apologies for the late reply. I have been out of the office on business travel the last few weeks.
> is it possible to use the save layer item that was saved in the 'My Content' in the Portal, on the AGOL environment?
Do you mean you want to "copy and move" the layer item from Portal for ArcGIS to an ArcGIS Online organization? I believe this is possible with Distributed Collaboration between the Portal for ArcGIS instance and an ArcGIS Online organization - but you may have to also copy the data source of the layer item as well. For more info, please see:
Distributed collaboration—ArcGIS Online Help | ArcGIS
> And is there a way to save all layer's configuration in the webmap at once as "an item" instead of one layer at a time?
No, this operation can only be done on a per layer basis.
> Is it a normal practice to have services coming from Portal/server, but have the webmap and webapp in AGOL rather than Portal?
Yes, this is a very common workflow/practice. Many organizations prefer to host their data and web services within their own infrastructure, but leverage ArcGIS Online as their "front end" to host web maps and apps.
Hope this helps,