There have been several threads recently in 'chat' or 'AIBU' about universal credit and the changes it will bring.
So yes you can apply for WTC/CTC if you currently meet the criteria, but the expectation is that when universal credit is introduced there is an expectation that any claimant will be working towards increasing their income, and reducing reliance on UC. One possible outcome is that if your income from your company is less than minimum wage, then you might be expected to transfer to a minimum wage job, if one were available, or if you worked less than 30 hours, you might be expected to either increase your hours in your current role, or take a job that offered more hours (depending on the age of your children, I think). If you didn't want to do wither of those, and wanted to stay in your current role then you might risk losing your uc.
If you have a small limited business, your salary can be made up of wages, and directors dividends related to the profits. You should be able to claim. Hopefully MrAnchovy will be here soon to clarify.
Greatwork is correct with regards to the change with UC, but if you get your claim in soon then you should be able to get on the 'old' system which should give you a couple of years to bring your income up anyway. Also, I think you might well be able to use evidence of how you are trying to increase your earnings through the business to bring it up to nmw levels. Finally, even if you loose UC due to low incomes you loose the personal part not the childcare from what I've read so far. (We are in a similar situation so have been researching quite a lot.)