I don't think that's necessarily a problem, in fact it can be a useful tool: if the slapped notes are much louder then the apoyando ones than you have a powerful means of giving your lines dynamic scope: congratulations! Of course, the result may be that your bandmates get all annoyed about you slapping murderous volume levels in their faces, and forbid you to do any slapping at all without first turning your level down, is it that?
Fortunately, too much dynamic range is far easier to counter than too little: that's exactly what any compressor does! And having a compressor on the bass is usually considered benefitial anyway, the only real problem being that it sacrifies dynamic range. So maybe that's just what you need. If a normal compressor (sidechain low-cut might be handy) won't solve the problem adequately, perhaps a multiband one will (e.g. EBS MultiComp); such a compressor brings the sounds even closer together by specifically reducing the strong treble components of the slap notes, while avoiding that these notes loose their groove qualities. Instead of an actual compressor, simply saturating the amp more strongly and/or reducing the treble may also do the trick, but you won't be able to get a really clean hard crisp slap sound anymore with that method.
Regarding your playing technique itself: slap is pretty much intrinsically loud, not much to be done about that; but mayhaps your fingering could do with a bit more power? It is quite possible to achieve the same volume with apoyando and slap, with only the treble component as a difference. In fact, the little slap technique that I can do has difficulties competing with my flamenco-picado-ish finger technique, but that's of course more because I can't slap, not because I have a particularly strong apoyando. Still, perhaps you could do something about that – plugging closer to the bridge, playing "deeper" with your fingers on the next strings... Perhaps you need to set your strings a bit higher, perhaps you should change your pickup balance (if possible).