Hmm...I think you would want to use your second choice. Apart from would mean we are not considering it in our conclusion. Apart from the accident I had, it was a lovely day! Apart from the one cold and windy day last week, this month has been very warm! It would be saying to disregard what is "apart from." We would not use it with also. Your second sentence is fine. Besides that just means in addition to. I agree with Maryalana.

1. Other than that we also discussed how to make projects. 2. In addition to that we also discussed how to make projects. They are synonyms (same or nearly the same meaning as the other), both mean “in addition” but “apart from” also means “with the exception of”. Apart from is exclusive and besides is inclusive. Hope someone else can explain it clearer!