Entry clearance paperwork question

I am filling out the visa application for entry clearance.
I am filing as a work permit holder...
On the application it asks you about employment now and your work permit employment in uk.

What if I am not working at all until I get my entry clearance in uk will they hold this against me?

No - don't worry about it.  As long as you have the work permit you are fine.   I wasn't working at all when I applied for mine.