I mostly agree with dusordua on the differences between UA and EK. Although if you are going to fly the airline enough to earn status then I believe it is nice to have it when flying them as your partner status will not get you anything. I am a UA 1K and will be flying EK a lot more in the future and I noticed that the bonues for C/J and F where better if I deposited to a Skywards account than if I deposited to my UA account. I could also use those for upgrades later so once I got enough miles I could just purchase C/J instead of F and upgrade. I could not do that if I put the miles in my UA account.

I do think it is good to concentrate on a few flyer accounts instead of distributing miles in many accounts but generally you will get more out of crediting the miles to that airlines account especially if you add in bonuses and not just premium class bonuses but promotions they sometime run. If it was a small amount of miles you are going to fly with an airline I would suggest you just stick the miles in the partner account but as many miles as you mentioned I would consider leaving them in your skywards account and using them for upgrades.