In this story I've started, the bad guy is doing a lot of stuff in the background that the main character isn't to know about until the end.
Part of this is all to do with how the bad guy tracks down and finally meets up with the good guy.
LOL - bad guys, good guys. Sorry, but I'm trying to keep this simple without having to write the whole of the novel out here so you get the idea.

Anyways, I'm pretty sure that the best way to explain what's going on is to switch PoV and have some very small chapters which tell what the bad guy is getting up to in relevance to the timeline of the rest of the story. However, I know that there's a lot of advise saying to stick with 1 PoV.

The only other way I could do it is wait until the end & the two characters meet up & then have all the stuff that the bad guy has been up to come out in one big go. This would mean that a lot of things get explained at the end, but a lot of it would sound like too much coincedence.

I think it would work out better the first way around.

So go with the first. There's no reason why you can't, unless you're writing the novel in first person. Then you absolutely must hold back that information. (But there are other ways of gently bringing it in with first person narrative without the classic villian spills everything at the end routine.)

May I recommend that you do something known as a novel or story diagramming (mapping)? This way you can see how it has been done before and if it is something you'd like to try.

Take a good book that does what you would like to do and make a brief chap by chap outline of what happened and then go back and make notes of what you liked and didn't like.

A great book I think that does what you are talking about is In the Corner of His Eye (or was it Out of the Corner of his Eye) by Dean Koontz.

Although: switching POV doesn't work well in short stories (in most cases there are exceptions)

JB Skaggs

1) Changing character POV - changing the character who is telling the story

OR

2) Changing the story voice - switching back and forth between first person and third person limited (for example)

While changing narrators can be fairly seamless (even in first person, if done well), changing narrative voice can be jolting and confusing -- it can be done, but it is difficult to do well even by experienced writers and is therefore not recommended.