1) Is it possible down payment thro APP? Please give me complete process.

In APP "set up all company code" step there is a field for specify special G/L indicator for
vendor and customer. you specify there special G/L indicator "A" & F. them make the 
process as it is. then make a down payment request through  t code F-47. then at the time of
APP run system  automatically pay the amount for down payment.

2) Tell me the process of making partial payment from APP?

we have to assign the terms of payment (instalment terms) to the vendor, based on this terms
we can pay partial amounts to vendors in APP.