I want to Split the payments into 45%, 45% and 10% of all Invoices due only to the specific supplier/vendor(Example: IBM)? How to Implement it. Can someone help me.

I am not sure if I understand this correctly. Lets say you have 20 invoices due for IBM, you wish to pay 45% of these invoices now, 45% some point later and the rest 10% of the amounts yet at another point in future. To implement this you would create a payment term with 45,45,10 split and assign it manually to all outstanding invoices for this supplier. You can also assign this term to the supplier and sites but this will only be defaulted down to future invoices.

Sorry my bad, I didn't put it correctly. All Invoices Due on same period(monthly), Instead of Printing One Check. Supplier wants it in 3 Checks(45%, 45% and 10%). I think it's not possibile. Any suggestions, please let me know.

You can still do it using the same method. Apply the three line payment term (45%, 45%, 10%) to all the invoices belonging to this supplier manually. This will produce three lines per invoice in the Scheduled Payment screen. You goal is to pick the first set of lines in first pay run, the second set of lines in the second pay run and the third set of lines in the third pay run. Each pay run will produce one check. You can do that either by making use of Priority field in the Scheduled Payments screen. Priority is one of the criteria you can use to filter scheduled payment for the pay run. Alternatively you can play around with the Pay Through Date so that only those lines are picked up that are due on a certain date. You can make the first set of lines due in 30 days and the second set in 45 and so on.