Hello and welcome to the Captivate forum,
Since you are referring to master slides, I suppose that you are using version 5?
I'm not sure to understand all your questions correctly, will try to give you some answers, but perhaps not what you expected.
First of all: each project in CP needs one resolution, you will not be able to mix different resolutions. If you want to capture at a resolution that is not in the dropdown list in the dialog box for recording, choose 'Custom size' and you will be able to type width and height in pixels.
You want to apply a master slide to the captured slides? If you want to have the master objects on top you can activate this in the General accordion of the Properties panel of the slide (see screenshot). But I'm not sure this will give the wanted effect.
If you want to have some part of the master slide surrounding your captured area you can resize the project later on and apply then the master slide. I explained something similar in this blog post:
this is what exactly i needed.
I have some more question:
1, we have to resize all recorded slides in your way (suppose recorded slied is more than 100. we have to change the 100 slides?)
2,we are using captivate 5 we cant change the custom size while using our templates.
I tried to explain that you can only have one resolution in a file, so all your slides need to have the same resolution, dimensions in pixels. That is why you never rescale one slide, you always rescale a project. Look in the menu 'Modify', where you will find the option 'Rescale project'. And please, have a look at the blog post I mentioned, the workflow is explained there.
You can capture in one file, rescale it and apply the Knockout Master slide to the captured slides, then add slides which are not captured and apply a similar master slide to it, but perhaps without the 'knockout hole'?