I cannot find how to save SIP account ids for correct using of it by KCall and Twinkle. Should it be some of phone numbers or instant messengers?

I suspect that you may not be able to, but it's certainly worth experimenting. Saving as an IM won't be any good to you, I think, because if you look at adding one, you'll find that you are expected to choose a protocol, and SIP isn't included. That more or less leaves Telephone numbers. Certainly you could store it there, perhaps choosing Messengers as the label, but whether KCall or Twinkle could use them, I don't know.

Of course if you know that one of the protocols listed is SIP-enabled that's a different matter.

What might just work is to have a normal addressbook entry, such as

John Smith
Tel: blah blah
etc

then

John Smith SIP
tel: SIP number

Then point your apps to that second account.

I guess SIP phones are just too new for KMail's structure. It's probably worth asking the developers whether this feature is planned for the akonadised KMail, so that you can file a bug/wish for it if they haven't already considered it.