I've never had any experience with using SATA drives with Windows 98, but I do know that if you ever need WIndows 9x drivers for these types of cards, this website has them:
http://toastytech.com/files/w95stuff.html

Also, some VIA SATA controllers don't play nice with SATA v2/3 hard drives without a compatibility jumper, not sure if your Syba PCI card is affected.

I'd try the motherboard's integrated SATA controller first, that way you know if it really is running in IDE mode or if it uses RAID mode, IIRC SATA controllers in IDE mode will function as a tertiary and quaternary IDE controllers. However, I remember hearing that some modifications are required for Windows 98 to work properly with more than two IDE controllers active. If for some weird reason the motherboard's integrated SATA controller doesn't allow mode changing or doesn't work with your hard drive(s), then I'd try the PCI controller, or use either a SATA-to-IDE adapter or an IDE hard drive as a last resort.

Excluding possible SATA2/3 issues, I have not had issues with that particular SATA controller on 98SE until the controller itself just stopped working one day.

If onboard SATA ports can be put to work in IDE mode there won't be any need for a separate controller other than LBA48 concerns. If BIOS has no LBA48 support and you use DOS with drive larger than 128GB there will be data corruption if anything past 128GB is accesed, even if windows itself gets the LBA48 patch. SATA controller will be free of this limit.

I couldn't get DMA to work with VT6421A in 98SE 🙁

There is no traditional IDE DMA per se on these addon cards, they always do bus mastering rather than normal IO cycles which are always going to be fast. Without a driver you will get access via DOS int which is slower but still way faster than traditional IO sequences. With a driver there's always PCI bus mastering based accesses which are what the DMA option normally enables in device manager for regular IDE controllers.

Thanks for reply!
I have installed the latest v6.10a driver for 98SE but got no DMA option at all.
The transfer speed is very good but the CPU usage is 98%

KCompRoom2000 wrote on 2018-04-20, 07:37:

I've never had any experience with using SATA drives with Windows 98, but I do know that if you ever need WIndows 9x drivers for […]
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I've never had any experience with using SATA drives with Windows 98, but I do know that if you ever need WIndows 9x drivers for these types of cards, this website has them:
http://toastytech.com/files/w95stuff.html

Also, some VIA SATA controllers don't play nice with SATA v2/3 hard drives without a compatibility jumper, not sure if your Syba PCI card is affected.

I'd try the motherboard's integrated SATA controller first, that way you know if it really is running in IDE mode or if it uses RAID mode, IIRC SATA controllers in IDE mode will function as a tertiary and quaternary IDE controllers. However, I remember hearing that some modifications are required for Windows 98 to work properly with more than two IDE controllers active. If for some weird reason the motherboard's integrated SATA controller doesn't allow mode changing or doesn't work with your hard drive(s), then I'd try the PCI controller, or use either a SATA-to-IDE adapter or an IDE hard drive as a last resort.

Thanks to your post, I managed to make Windows 98 SE work with an integreated SATA IDE port in DMA mode (VIA VT8237A), by limiting the number of controllers to two, and installing PTCHSATA, as detailed here: MSI MS-7253 / K9VGM-V (KM890, VIA8237A) , Athlon 64 X2 5050e, Radeon X800 XL . It works extremely well (also found out that by default DMA is not enabled in the disk properties, it must be enabled manually).