Using Airport Express as separate wifi network vs extender with Time Capsule?

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Hello all.  I recently converted my home computer network from Windows/PC based to an iMac with Time Capsule.  On my previous setup, I had a Cisco/Linksys router with wifi, and I also had two Airport Expresses in separate areas of the house where the Linksys had a weak signal.  Obviously, I had the Airport Expresses set up as "separate" wifi networks, as they could not be used as network extenders with the Linksys.  This setup seemed to work really good, as the 3 wifi networks provided good blanket coverage in all parts of the house.  Each network also seemed to "hand-off" to the other pretty well, meaning that Airport Express 1 would show as the active network when you moved far enough away from the Linksys (or insert any of the network names here, even though I'm pretty sure that the device accessing the network has more to do with this than the networks themselves).  In particular, the speeds that I got from the Airport Expresses actually eclipsed the speeds that I would get from the Linksys wifi.
My issue is that after I converted everything, I left the Airport Expresses as "separate networks" and essentially removed the Linksys/Cisco router and replaced it with the Time Capsule.  So I still have 3 separate wifi networks, just like before, with the Time Capsule network taking the place of the Linksys wifi network.  While the Linksys and the Airport Expresses seemed to co-exist together nicely, I get the feeling that the TC and the AEs are somehow working against each other or at least competing with each other for bandwidth.  For example, if I have my iPhone right beside my iMac and TC, and I run a speed test on the iPhone using the TC wifi network, I get download and upload speeds in the range that I am expecting (30-40 mbps download).  However, when I walk down the hallway to the other end of the house, the TC tends to remain the dominant wifi network, even when I am in the same room with one of the AEs (this is where they used to "hand off" nicely between networks).  When you run a speed test in this location still on the TC wifi, the speed drops down to 5-7 mbps, and worse, I believe the signal becomes inconsistent because webpages and data often seem to be freezing in the middle of downloading.  I understand that the distance from the TC is causing this, because my solution has been to manually switch from the TC to the closest AE, and that fixes the issue.  Run a speed test after I manually switch to the closest AE when I am in the same room as an AE, and the speeds pop back up to 30-40 mbps.
My question is this:  would switching the AEs to "extenders" of the TC wifi network help this issue?  Honestly, my laziness was one reason that I did not do this when I setup the TC initially, because I have several devices that access the AE wifi networks that I'd have to update with the new network name and password.  Everything was working great before, and I just didn't want to upset the apple cart.  But if I have created an unfriendly environment between the TC and the two AEs, I certainly have no problem making the change now.  I just wasn't sure if making this change would fix my problem or not.  I know it's a mundane thing, but I'd like to be able to roam the house without continuously having to manually switch between wifi networks to get a consistent signal.
Sorry if this is a simple issue.  I am admittedly a newbie with the TC and its interaction with the AEs. 
Thanks in advance!!
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It is not a simple issue.
Exactly which method works best is going to take some experimentation.
The way you are trying to set it up as a roaming network is generally considered the best.. but the devices like iphones do not hand off neatly.
It is interesting that they in fact used to hand off better using the Linksys.. which could be due to its poorer range. The new TC having so much better range is causing the phones to not swap "towers" to the local express.
Test it with a Mac laptop.. as generally they do hand off better.
I cannot quite figure out if you are using roaming correctly. All the wireless should have identical names, with identical security setting and passwords.
The only thing that should be different is wireless channels on each item. And you are likely just using auto anyway.
So each device is creating a wireless network. And for 2.4ghz one should be channel 1, then another channel 6 and another channel 11. For 5ghz it will be same idea but there are more channels available.
When you extend wireless, everything runs the same channel. But the wireless speed is reduced. You must disconnect ethernet to each of the expresses.. and the problem is your 30-40mbps will reduce permanently to 15-20mbps for all clients. So take your choice.. 15-20mbps for all clients forced to double hop is better than 5-7mbps which you experience now when you walk around.. although I am not sure how much browsing you do whilst walking. You may need to compromise which is the better out of several not great alternatives.
I would have a test.. which is wrong btw.. but I have heard that it works.
In your roaming network at the present time. Try setting each router to a manual wireless channel.. and fix all of them the same. So for instance, set 2.4ghz to channel 11. Try fixing the 5ghz as well, say the TC is defaulting to 149, it might not actually respond to manual wireless channels.. you will need to test this.. say set to 36 or 40 and see if the TC is actually changed.. if not just set all the expresses to 149 as well. What you are doing is trying to reinforce the wireless in each area.. but this is actually wrong. So all will have same wireless name and same security wpa2 personal is the only valid one.. and all the same password.
Test with a few clients and see if the results give you decent local speeds as well as better roaming.. once you decide which to do, then you will need to change all the clients.