Difference between ATO and PTO in oracle apps

1) MAKE TO ORDER: This is based on Customer specification, you make the product and supply it to them. This is applicable for Engineering items or any Product which you can make based on Customer order

Example: Engineering Items

2) ASSEMBLE TO ORDER: This is you have items in parts and it needs to be assembled according to customer requirements

For example you have Laptop coming with standard configuration of 160GB Hard disk and 1 GB RAM. But there are customer orders coming in asking for 200GB Hard Disk and 2 GB RAM and if you can assemble them to suit Customer Requirement

3) CONFIGURE TO ORDER: This is Configuring the Product itself to suit
Customer requirements

Example. The Thread Manufacturing unit Machineries are configured. I have seen Laxmi Machine Works in INDIA which manufactures textile Machineries configure the machineries based on No.of spindles

4) PICK TO ORDER: This is same as Computer Example in ATO. But the 
difference is the Customer will supply the items in parts to you and you
have to assemble at your own place. (i.e) Customer premises

5) ENGINEER TO ORDER: This is for AIRLINE and SHIP BUILDING based on Customer engineering Drawings

6) MAKE TO STOCK: Standard Components made and readily available for Sale. Example: Mobile, DVD, TV etc.,

If you look at the time Vs Complexity in XY Chart it is as follows

MTS, ATO, PTO, MTO, CTO, ETO

If you need more explanation refer Oracle E-Business Suite Supply chain
Book published by Oracle Press