Generally speaking I will use them together. This may duplicate some warnings in the Professional Chameleon (the freebie does not do that warning stuff) .. I tend to not mind dup warnings, anyway. In fact, I think I may have Anvir giving warnings on one puter or user as well. (To be fair, it seems to do so in rather a pleasant and informative manner.) Sometimes I may let one product drift off of current usage.
I do consider WinPatrol and Chameleon as reasonably complimentary. WinPatrol is heavily oriented to security and ferreting out all possible startup problems .. Chameleon (and also Metaproducts Startup Organizer, which does do warnings in an interesting manner where it puts all the changes in one box if it has been asleep for awhile, quite impressive) is more designed to user experience enhancements, simple visibilities, changes to startup, configurations, delays, etc. Plus Evgeni's person support and pleasantness behind the product.
On the whole, Startup is a high priority security area, so I do not mind a bit of extra, even redundant, visibility and coverage, (You do not make too many changes a day anyway, so redundancy is not a real problem.) I do not get into all the shadow and imaging and restoring stuff, I simply like my puter to be running good and I try to remember to save the data externally if something goes wrong, and I keep early images only. The last few years have been thankfully mostly trouble-free, using layered security.
Note: I am not really encouraging more than one, I am just saying it works fine, it is not like anti-virus and task priority or shadow/virtual systems and many other areas where the playground gets messy. Overall, I do think that startup is underrated in terms of security visibility and significance and that it rates right with firewall and browser care (security is hard to make into categories, HIPS, anti-virus, etc.) Only the dedicated startup programs really understand how it works and the security suites are dubious in this area.
Bill at WinPatrol makes startup security his key, even looking at things like "IE Helpers" and the Windows Scheduler and secret and difficult hiding places floating around the registry or wherever, always looking for the latest baddie methods. (Evgeni origiinally did not do services, and has it in the new task manager product, so you would need both startup and task for the more complete Evgeni support). The biggest concern is that it is hard for these, even in pro versions, to be "zero-moment" protection, against the type of malware that forces an immediate reboot. That is why you have to have good internet and .exe sense.
Overall, I do recommend going "professional" in one of the better programs and would never recommend a happy WinPatrol user to do a replacement ... security trumps startup ease and I do not place any other program quite up there with WinPatrol in that category.
As to security warnings, I will say that (this is not startup) MBAM - Malwarwebytes - seems to give some of the very best HIPS-oriented, I only noted that it can be, at times, a CPU hog. I am talking about the realtime mode, which I have played with the last months after some deal, rather than just on-demand scanning.