I tend to wait about 30 seconds and check if most of it's dissolved. Some times it doesn't completely dissolve, so I just roll my tongue beneath my lower lip and smoosh it until it's more granular. That usually does the trick. It's hard to keep it all beneath my tongue when I do this, but I don't think it's really a big deal.
Also, if you're being checked by your endo regularly (which is ~2-3 months for me), they'll likely prescribe a higher dose depending on the development of your levels. So even if you decide to just swallow the pill(s), your prescription can be increased to counter the reduction in effectiveness relative to taking them sublingaully (assuming your e is lower than it should be).