Boats should be with Maritime Security Agency patrolling coasts of Pakistan. You are talking about these boats.
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Those will be waayyyy down south as you can see.
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In order to use them up north in Rajanpur area, Punjab government should have approached Federal government who would order Navy to position those boats in that specific area. To position them they could either be transported by road (best way) or sail upstream in Indus crossing three major barrages (not so good option). Navy does however keeps some boats which could be quickly deployed and would be more than sufficient for the job. Here is an example.
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However what really happened is beyond incompetence of civilian agencies. Under strict instructions not to even inform military, Police chief orders district police to launch the operation. True to traditions of civilian institutions of Pakistan, he makes no arrangements to provide or arrange for the policemen what they need. He just threatens them and makes them launch the operation within two days. They beg for time and resources to prepare. Local police asks for a plan to gradually squeeze the outlaws into a pocket and then launch the attack. A fair plan in my assessment. Police chief who takes direct orders from brother of prime minister, scolds them, calls them cowards and pushes them into operation. And then he flies back to mega city of Lahore.
With meagre resources and foolish order to just charge in, what district police came up with, is this.
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They hire fishermen boats in haste. Policemen volunteer to go on this fatal trip. Rest is history!
You can blame military all you want, they were never asked to do anything. Under the constitution, military can be ordered to assist civilian government. But military can not just barge in on its own. People cry foul then, you know.