Yes, it will undermine your study a bit if you use 2 SRS programs to study the same facts. The whole idea of spaced repetition is to learn to the edge of forgetting. The software is designed to try to push your memory out to its limits-- it can't do that if you're busy *actively* reviewing. (As opposed to passive reviewing, which would be reading stuff in Japanese. That's fine.) The whole idea is to let the computer figure out how long you need to go before you need to see the stuff you're trying to remember again.

I tried using 2 SRS programs in the same fashion, and I found it really hurt my retention over time. But like I said, reading Japanese is a whole different thing, since it's a passive sort of review. Any good SRS program will have options for you to mark things that are way too easy for you to remember, so it can space them out further into the future. (The Easy button here.)

I use this site for RTK, and Anki for everything else. That way works just fine. Or you can just dump everything into Anki or some other SRS.

I have to use two SRS programs just to keep any sort of retention, at the moment. I understand the idea of spaced repetition, but I don't have the desire to wait that long until I'm finished with the book, and the fact that I'm learning over 100 kanji each day demands more repetition than one SRS can provide. Once I'm finished with the book, it's likely enough I'll swap over to only one SRS to maintain my kanji, but while I'm learning the rate I'm going isn't possible without an unusual amount of review. My mind is unusually geared toward this sort of learning, though (stroke patterns and things), as should be obvious by the number of kanji I'm managing to retain, and the fact that I'm not actually using images (that would take so much longer) or any other of Heisig's prescribed methods in using his book, so I can't necessarily advise this I may end up regretting it later, but so far it's working out for me. I've been studying Japanese for some time, and learning the Kanji at an incredibly slow (if steady) rate with their readings and example words, but finally decided enough was enough and I needed to know ALL the Kanji, NOW, and have completely put all other Japanese study on hold for this, so getting it all out of the way as fast as possible so I can start actively using my Japanese again is my only goal.

Heres an idea, but I have no idea if its possible. Seeing as the king kanji has all the files for RTK1, is it posible to export that to an srs for use on a PDA? for example from king kanji into anki/stackz/whatever. If only king kanji had a real srs function too...man if they add that they would be onto a winner!