My husband worked away Mon-Fri for the first 8 months (came back weds evening but only about half an hour before bedtime which was more a hindrance than a help), so that colours my view, but specific challenges....
As I say, going from being totally organised and in control to exactly the opposite. Shopping was a nightmare (toilets, shoes, coats, into the car... Sounds easy hut I longed for the days of just nipping to the shop quickly)
Managing 4 diaries instead of 2. The amount of paperwork churned out by the school has to be seen to be believed.
Trying to discipline 2 children who don't give a damn about having things taken away from themselves (they had nothing before, not food or clothes, so why worry about a teddy being removed?) and aren't attached to you, so couldn't give a toss if they upset you/make you cross.
The slow, slow progress . I have done 2x5 min sessions everyday on times tables with my kids for 4 months. They still can't score more than 3 out of 10 on a school test. We're taking 2, 5 and 10 times tables here.
DD waking up crying several times a night every night through anxiety (as we now know it to be). She was 5 when placed, fully articulate in some ways, but we couldn't soothe her fears with words, it just took time. It was very frustrating/tiring
Difficulties now? It seems one is always 'up' and one is 'down'... I mean by that, one is always regulated, the other disregulated and 'acting up'. Rare is the day when both are settled.
That being said... I'd still choose siblings over a single any day of the week and don't regret it at all.