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Source: https://writers.stackexchange.com/a/25155
License name: CC BY-SA 3.0
License URL: https://creativecommons.org/licenses/by-sa/3.0/

This doesn't have to be a problem at all. A "B" plot is an opportunity to enhance the main story by setting it off with something that feels a bit different and gives the reader some variety.

It's generally not a good idea to underestimate readers. Most of them are perfectly capable of understanding that, in this book we're gonna follow along with more than one character. (Some have handfuls of them and do fine.) However, it's also nice when we make things _easy_ for the reader. Dropping in very occasional references to ground the reader can do this. A few random suggestions as to the type of thing I mean:

- Maybe the chapters with the B mission simply _feel_ different. The pacing might be a bit different due to the timescale. 
- Perhaps the lead agent simply has a different personality to your main protagonist or speaks differently. 
- Is the weather different? 
- Maybe there's one plot in Shanghai and one in a small town in Russia, or a farm in South America. 
- Perhaps the action is of a different type. An action-oriented mission versus, say, a hacking plot or getting financial evidence can be a nice contrast. 

If you avoid being clunky and obvious about it - please avoid starting each chapter with "The agent said, through his ski mask" - and keep your references to ones that also advance the story, you should avoid any confusion and keep things moving along nicely.

Original score: 1