Do anybody have suggestion or same experience ? I already remember many kanji without mnemonic but usually forget. How to learn with Heisig method in this case?

I think approach should be the same as in this case: http://forum.koohii.com/showthread.php?tid=210
Remembering kanjis already will enable you to progress faster, extra effort for already known kanji being attaching a story to it and reviewing it several times.
What is remembered first (parts of kanji itself or story for keyword) is not definitive, as these two things reinforce each other.

I think you should just start in the beginning and work your way through. The book is arranged in a way so that kanji with similar primitives are grouped together, not by how common they are. A major goal of the book is to teach you the technique called "imaginative imagery," and that is covered in the first 400 or so kanji where Heisig supplies you with stories.

Since you already know 1000+ kanji, you'll just complete the book alot faster than most. But you'll probably find that when you finish the book, regardless of the amount of previous kanji knowledge you've had, you'll be able write and recall the kanji more quickly and accurately because of your increased knowledge of primitives. Also, this knowledge of primitives will help you learn new kanji outside of the book later.

I agree with just starting at the beginning and trying to learn the method in the book. You say you know over 1000 kanji, but often forget. If you stick with the book you'll see all the kanji you know in a new light which will make them hard to forget.
I'd also trust the reviewing on this website. Study a chapter, add it to the site and review when it tells you too. Within a week you'll already be focussing more on the kanji you don't know well enough (although you will have some long boring reviews to get the easy kanji up into higher boxes...)

I knew about 600-700 kanji (with readings) shakily before I decided to really give this book ago, and I systematically went through each character anyway, even if it was one I'd seen hundreds of times. I think that's the most sensible way to go.

And the ones you already know will be extra easy to remember because you've already studied them, so it's not like you're wasting all the time you've already spent learning kanji.