I was planning to use the Dual mode, but I can only have one algorithm for each insert max.
Inserts are not available in Dual mode, so I assume you mean signal path. In Dual Mode you may place one algorithm per path, or two on Path 1 only, or two on Path 2 only.
I was surprised that the programs I already made in insert mode were not available
The manual states that all programs created in the Insert Global Routing mode will not be available in Dual Routing, since the signal flow architecture is different.
I was thinking of using the insert mode and plugging the mic in input one and the pickup in insert two. I get a level difference issue.
Are you using preamps for your mic and pickups? Do you have a way of adjusting levels for these capturing devices? Pickups tend to be high-impedance (Hi-Z) instrument level signals where mics tend to be +4 dBu or -10 dB line level depending on the model of preamp. A preamp helps convert to the appropriate signal type, which for line level is -10 dB. Make sure the I/O in the System Menu of the H90 is set for line level on the inputs for the mic and set to instrument level for the pickup.