When you pay a EUR invoice into a EUR account QF will apply a rate that is pulled from xe.com to work out the GBP equivalent. This GBP amount can be overridden when you lodge the payment.
Now when you exchange EUR to GBP QuickFile will also allow to specify a GBP value on the receiving end. This may leave a currency loss/gain sitting on the EUR account, typically what you would do then is periodically journals this out.
The journalling out process is described here: