It's usually a very bad idea to use your own tables. We have had to rewrite several projects we have inherited from other developer teams to convert custom tables into Elgg entities.
I can think of very few cases where that would be justified. First explore existing data model - entities, metadata, annotations and relationships. Most likely you can achieve your goals without having to maintain a separate table. You are bound to run into performance issues, access-related problems etc.
If you still have to, take a look at hypeGeo. It uses a custom table.
Seconded ^
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