Let me start by saying that i don’t think there is such a thing as ‘the correct way to go’ …in art everything goes as long as it suits you!
But to get in to your pipeline question (thats the ‘industry’ term for the sequence of programs you use ) to me it seems painfully long.
Starting in pap do some animating there then exporting your jpegs to photoshop color them there then after effects for the camera shots and special effects and then…finally going to premiere to edit it together.
i’m a professional 2D animator and i do all of these steps in one program called Mirage(TVP animator)
it is a bitmap type program and just like photoshop has layers and similar paint options but it also has a timeline like after effects and it lets you do effects and camera moves.
it is very suitable for 2D animation. the latest incarnation of it even has a rotating animation disk and a multiplane camera option
check it out: here
you can download a fully working 30 day demo(beta version) when you subscribe to the forum
mirage has a rapidly growing userbase and a great community of users