it sounds like she is coming into the uk as a 'visitor' but is living with you (& you are on work permit?) in the uk. This is probably the reason why you had problems with coming back from spain.
Assuming that you get the 'correct' visa for her (I've no idea what that is), then it doesn't matter how you enter the uk.
Immigration don't like people using a tourist visa system as a means to live permanently in the UK, so make sure you get the correct visa for her.
