A married couple who are living as such can only have one main residence between them. If you didn't make an election for one of those homes to be treated as your main home within two years of having two homes available to you, notwithstanding the fact that you don't own two, then when you sell one, the matter will be decided on the facts which may not necessarily result in your preference. Read the notes here
As of now, if you sell one of the properties and it is decided on the facts that it wasn't the main home from the date of your marriage, then part of the gain will be tax free and part will be taxable. The tax free part will be that proportion of the gain covered by the owner's occupation of it and the last 18 months of ownership of it (36 months prior to 6 April 2014). The balance of the gain will be taxable, though if it is sold in the 2015/16 tax year, the first £11,100 will be exempt.
There are two rates of Capital Gains Tax, 18% and 28%. The rate or combination of rates that will be paid will be dependent on the level of the income of the individual who makes the gain. Take a look here
for more information on determining the CGT rate, though these are for the 2013/14 tax year.
Give that the rate of CGT payable is determined by the level of the income of the seller, you might be able to reduce the CGT exposure if you put the house you want to be treated as your main home into joint names and your respective incomes aren't roughly the same. It has to be done when it is your main home, you are both living there and you are confident that you can argue that it is. If you can do that, then the individual who is added to the deeds will be taxed on half the taxable gain and will get the same amount of main residence relief as the original purchaser. That's one of the benefits of marriage. Read the notes here
for the specific conditions.
Take a look at HS283
for more information on the main home and CGT.
I hope this helps but let me know if you have any further questions.