The majority of the time, I feel like an awful mother b/c I can't spend equal time with both girls.
I completely understand how you feel Sabs. At our worst times my DS1 spent at least 3 hours a day watching DVD's while I tried in desperation to get DS2 to eat and/or sleep. At the time I felt like the most incompetent mother on the face of the planet.
Looking back if I had to do it again, even with the knowledge I have, I would do it all the same way. Why? Because you have to do what works when you have refluxers - and that includes the siblings and your spouse.
You are NOT an awful mother. You cannot spend equal time with your children ... ever. I thought it was possible, but it's not. There are some days I spend way more time with DS1 than DS2 and vice-versa. I would imagine that if I added up the minutes over a week, it would be pretty even. But to keep 'score' isn't going to help anyone. Your kids will not keep a tally. In fact you may find that 20 minutes total 1:1 time with Madi is enough to fill her 'Mummy-time' cup for a day. Another day she may need more.
Right now Alyssa is going to need more time because she is little and completely reliant on you for everything. As she gets older this will ease off.
Do make a point of spending some 1:1 direct time with Madi so she doesn't feel left out. I used to take DS1 out for a walk around the block just after DH got home so we got away from DS2 and I then only had DS1 to focus on.