What you describe is one proper way to check.
Whether the fields align when they are weaved together for computer display depends on which one is captured first. If they aren't already aligned, all you have to do is remove the first field (or add one to the start if that first field is somehow essential to you). The solution I always use is SeparateFields().Trim(1,0).Weave() but there are other ways to do the same thing.
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Warperus has mentioned another issue which is that you need to base the way you handle chroma on whether the encoder used progressive mode or interlaced mode.