Issue-How to book costs-Vendor Invoice

Hi,
I have got following scenario.
I got several POs raised for procuring goods from a vendor.
The vendor send the shipment combining these PO.
The goods are cleared by local agents(vendors) and they also charge for clearing the goods.
All these costs needs to be added on to the materials in PO so before actual GR,POs needs to be modified to incorporate those freight or clearing costs as conditions.
Once that is done then the GR is done & subsequently Invoicing is done.
While conditions were added the appropriate vendor is selected in the condition so that it will be different than the original goods supplier.
Now the problem which we face is that sometimes we receive partial shipment for the PO.
So we can book the additional costs only once while booking an invoice.
Take an example:
I have a PO with 100 line items.
I receive the shipment & local vendors clear the goods & while doing that I incurr say 100 USD cost.
This 100 USD cost comprises of 3types of different conditions defined like freight clearing,Demmurage cost,Others cost.
So before doing GR in system user adds these conditions as header conditions so that it gets apportioned on all items & subsequently upon GR it also gets loaded on to material.
Now assume that out of this PO, I have yet to receive delivery for 20 items.
So when these 20 items actually arrives on a later date, the local agents again clear those goods.
But since we are referrring to the same PO we can not add these 3 conditions again in the PO.
Now if we have to book an vendor invoice for that and at the same time I want thos costs to be added on all the materials how can I do that while doing MIRO.
If I happen to add them as unplanned delivery cost then I will have to manually split the cost on to each item depending upon the value of each line item which is practically a very difficult & painstaking task.
Is there any way by which we can improve upon this.So far we have not find any solution on this.
Request to suggest a better suggestion if any one has.
Thanks in advance
Regards,
BM

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and lets go to youe example
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Issue-How to book costs-Vendor Invoice

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