I don't think there's any tie up between Afghanistan and Pakistan team. When it comes to training. They might train in the same country, UAE but I don't think the Afghans train in Pakistan. It's a possibility though, they could train in Pakistan as well as in India as, the talented players get selected for the premier leagues of each country and they train with those respective teams.
In last two decades Pakistan have no good relationship with Afghanistan just because of this their cricket relationship is better with India instead of Pakistan, and they are going into IPL as well which is good platform for them as their nearly half dozen players are having good contracts and good money from them which is helping them in positive way.
Few months back they hired Umer Gul as bowling coach and now have Jonathan Trot an English man as their head coach but still they need the good number of matches for better results against big teams which is going to help them, but main problem is still there they can't play at home which is surely a concern and important hopefully we will have them as good team in near future in all formats.