It is common to use methanol or other aqueous miscible, stronger solvents to perform an initial extraction. However, reversed phase SPE requires the sample to be loaded in a mostly aqueous solution. You can either evaporate most of the methanol and dilute the sample with deionized water prior to sample loading, or simply dilute the sample with a lot of deionized water.
Ideally, the methanol composition of the sample should be <20% for loading. If the target analytes are particularly hydrophilic, the methanol content will need to be even lower (e.g. <10%).