Rather than enter them into your database first up, I would suggest that you extract the names with a good old pencil and paper method :-), This way you can look at family groups you may come across. For example, when you find a Christening, record the parents, with the child's name below. Leave enough space below each set of parents for about 6 or so children. Look for dates of marriages and burials. If they appear to match the names you have in the family group, record those beside the names - either for parents or the children. Keep recording the families in this fashion and you should start to see a pattern of relationship develop. It may show that you can link lines together, or you may find extraneous branches of the family which have no discernible links at all to the others. You can, if you wish draw lines on the page to link families (I use this method quite often).
Once you have sorted them in this fashion, then you will have a clearer picture of just who is related and who is not. Then you will be able to enter them into your database and keep the others on the paper record for future reference. Saves a lot of typing of unnecessary names and details.