Can anyone tell me the actual difference between ISUP and ISDN call and how do we decide which one to use? Question is very basic but i always find difficult to understand.
ISDN is a set of standards for voice, video and data communications over traditional circuit switched networks.
It includes standards for the protocols between the end devices (e.g. phone) and the switch in the public network and standards for the signalling between one switch and another in the public network.
ISUP is part of the suite and is a protocol that is used between switches in the public network - often called trunk calls, or more accurately trunk legs of an end to end call.
So strictly speaking an ISDN call is any call which includes ISDN end points and signalling and an ISUP call is a specific connection between two points (usually public switches) which uses the ISUP signalling system.
As the internet emerged and evolved, some of this technology also made its way into the VoIP world with some VoIP signalling growing out of ISUP signalling for example - specifically BICC (Bearer Independent Call Control).
I suspect that knowing this you may now have a different question, so fire away...
Update
ISDN standards include two access protocols, BRI and PRI.
BRI is Basic Rate access and is targeted at residential and small business and provides two voice channels and one data channel.
PRI is Primary rate access and is targeted at business with PABX's (their own internal switchboards). It provides either 23 voice channels and one data channel in North America, or 30 voice channels and one data channel in Europe.
This was all designed in the days before the internet and ADSL so it was seen at the time as way to provide higher speed data to subscribers while still allowing them make calls. Dial up modems took over the whole subscriber line so calls could not be made.
ISDN BRI was never particularly popular and when the internet arrived it became even less so.
ISDN PRI was used quite heavily for connecting PABX's to the public network.
For your situation, it sounds like you have a modern public network which is using Call Servers and Media Gateways. The Media Gateways terminate the subscriber lines and convert from the TDM access world, into the public backbone network (which is mostly likely IP, MPLS or ATM in your case). The Media gateways also terminate trunk calls from traditional TDM switches in older public networks.
Calls you are seeing with an ISDN setup message are likely from PABX connections, although they could be from BRI lines.
Calls with ISUP IAM messages are most likely from older TDM switches connecting into the newer Call Server and Media Gateway network - i.e. Trunk calls.