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Double thump and switching strings?

I'm working on my double thump proficiency. Things seem to be okay but I realized that in a particular case I'm not sure what I should be doing or if the technique is even used in such a scenario. I have been working with running scales with doing the down up with the thumb but not hitting the same note on both. ie if I was playing G major starting on the E string I'd do down on G, up on A, (move to the A string) down on B up on C etc.

But without having even number of notes on a string before I move up or down some problems arise. For example continuing the above pattern I am hitting down on D on the A string but the next note would be an up on the E on the D string. This is awkward and at this point feels like it takes a lot of time and I'm unsure if I could ever make it smooth. The other problem is when I'm descending and have a down followed by an up on the subsequent lower string.

I was looking back over Wooten's tutorials and it doesn't seem like he is ever explicitly suggesting using the technique in this scenario, rather it seems like it is mostly doing down up on each note. So my question is, is anybody able to successfully use this technique in this scenario? I just don't know if I should persevere or if this is a natural problem that doesn't have a good solution