You have a few options.
1) The least head-achey one would probably be to install a9lh, and then just follow the following guide to autoboot into your gateway emunand (as mentioned earlier):
https://gbatemp.net/threads/tutorial-using-luma3ds-with-gateway-on-v2-a9lh.431691/
2) the most future-proof one would be to take your saves from your games in gateway emunand (using jk's savemanager), install a9lh, and then just attach your NNID to your sysnand and redownload your games. Get rid of emunand by formatting your sd card, and get rid of gateway/sell it. Only downside is you might lose saves/puzzle pieces/streetpass folk. Upside is you get to start fresh and any gateway tomfoolery won't trip you up down the road.
3) You...should be able to follow the a9lh guide and in the process, flash your gateway emunand and make that your sysnand. I'm not sure how advisable that is, and would recommend to wait on that until someone with more know-how can advise.
Personally, I'd go with 2, and just use the gateway bluecard as a ds romcart. With a9lh you don't need emunand anymore, basically. But there are choices =]